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#19908 new defect

ChimeraX bug report submission

Reported by:	z.campbell@…	Owned by:
Priority:	normal	Milestone:
Component:	Unassigned	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:
Project:

Description

The following bug report has been submitted:
Platform:        macOS-26.3-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
With a chimera session open, walk away from the computer long enough that it goes to sleep. Upon returning, wake up the computer and focus on the chimerax window. Until "show this message again" is unticked, clicking "ok" on the error prompt just causes it to endlessly reappear.

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/20260217_FinaldensitiesWIP.cxs
> format session

Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 0 as #11.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 1 as #11.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 2 as #11.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 3 as #11.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 4 as #11.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 0 as #12.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 1 as #12.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 2 as #12.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 3 as #12.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 4 as #12.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 5 as #12.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 6 as #12.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 0 as #13.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 1 as #13.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 2 as #13.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 3 as #13.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 0 as #14.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 1 as #14.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 2 as #14.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 3 as #14.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 4 as #14.5, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 0 as #15.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 1 as #15.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 2 as #15.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 3 as #15.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 4 as #15.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 5 as #15.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 6 as #15.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 0 as #16.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 1 as #16.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 2 as #16.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 3 as #16.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 4 as #16.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 5 as #16.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 6 as #16.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 0 as #17.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 1 as #17.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 2 as #17.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 3 as #17.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 4 as #17.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 5 as #17.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened 60S_filtsharp.mrc as #1, grid size 270,270,270, pixel 2.59, shown at
level 0.00474, step 1, values float32  
Opened Decoding_filtsharp.mrc as #2, grid size 270,270,270, pixel 2.59, shown
at level 0.00591, step 1, values float32  
Opened Hibernating_filtsharp.mrc as #3, grid size 270,270,270, pixel 2.59,
shown at level 0.00507, step 1, values float32  
Opened Int_Post_filtsharp.mrc as #4, grid size 270,270,270, pixel 2.59, shown
at level 0.00705, step 1, values float32  
Opened Post_filtsharp.mrc as #5, grid size 270,270,270, pixel 2.59, shown at
level 0.00678, step 1, values float32  
Opened Rotated_filtlocal.mrc as #6, grid size 270,270,270, pixel 2.59, shown
at level 0.00572, step 1, values float32  
Opened Translocating_filtsharp.mrc as #7, grid size 270,270,270, pixel 2.59,
shown at level 0.00737, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc as #8, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_none_filtsharp.mrc as #9, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened Hibernating_filtsharp.mrc 0 as #20.1, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 1 as #20.2, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 2 as #20.3, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 3 as #20.4, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 4 as #20.5, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 5 as #20.6, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Int_Post_filtsharp.mrc 0 as #19.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 1 as #19.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 2 as #19.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 3 as #19.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 4 as #19.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 5 as #19.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Post_filtsharp.mrc 0 as #21.1, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Post_filtsharp.mrc 1 as #21.2, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Post_filtsharp.mrc 2 as #21.3, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Post_filtsharp.mrc 3 as #21.4, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Rotated_filtlocal.mrc 0 as #22.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 1 as #22.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 2 as #22.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 3 as #22.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 4 as #22.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Translocating_filtsharp.mrc 0 as #23.1, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 1 as #23.2, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 2 as #23.3, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 3 as #23.4, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 4 as #23.5, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 5 as #23.6, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 0 as #24.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 1 as #24.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 2 as #24.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 3 as #24.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 4 as #24.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 5 as #24.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 6 as #24.7, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 0 as #25.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 1 as #25.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 2 as #25.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 3 as #25.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 4 as #25.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 5 as #25.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened Decoding_filtsharp.mrc 0 as #26.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 1 as #26.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 2 as #26.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 3 as #26.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 4 as #26.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 5 as #26.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 6 as #26.7, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 0 as #18.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 1 as #18.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 2 as #18.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 3 as #18.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 4 as #18.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 5 as #18.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened Rotated_filt.mrc as #10, grid size 270,270,270, pixel 2.59, shown at
level 0.00669, step 1, values float32  
Opened Rotated_filt.mrc 0 as #27.1, grid size 270,270,270, pixel 2.59, shown
at level 0.00669, step 1, values float32  
Opened Rotated_filt.mrc 1 as #27.2, grid size 270,270,270, pixel 2.59, shown
at level 0.00669, step 1, values float32  
Opened Rotated_filt.mrc 2 as #27.3, grid size 270,270,270, pixel 2.59, shown
at level 0.00669, step 1, values float32  
Opened Rotated_filt.mrc 3 as #27.4, grid size 270,270,270, pixel 2.59, shown
at level 0.00669, step 1, values float32  
Opened Rotated_filt.mrc 4 as #27.5, grid size 270,270,270, pixel 2.59, shown
at level 0.00669, step 1, values float32  

Not registering illegal selector name "40S"  

Log from Fri Feb 20 15:29:20 2026UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/rotationWIP.cxs

Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 0 as #11.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 1 as #11.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 2 as #11.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 3 as #11.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 4 as #11.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 0 as #12.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 1 as #12.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 2 as #12.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 3 as #12.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 4 as #12.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 5 as #12.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 6 as #12.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 0 as #13.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 1 as #13.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 2 as #13.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 3 as #13.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 0 as #14.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 1 as #14.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 2 as #14.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 3 as #14.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 4 as #14.5, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 0 as #15.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 1 as #15.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 2 as #15.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 3 as #15.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 4 as #15.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 5 as #15.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 6 as #15.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 0 as #16.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 1 as #16.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 2 as #16.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 3 as #16.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 4 as #16.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 5 as #16.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 6 as #16.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 0 as #17.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 1 as #17.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 2 as #17.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 3 as #17.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 4 as #17.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 5 as #17.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened 60S_filtsharp.mrc as #1, grid size 270,270,270, pixel 2.59, shown at
level 0.00474, step 1, values float32  
Opened Decoding_filtsharp.mrc as #2, grid size 270,270,270, pixel 2.59, shown
at level 0.00591, step 1, values float32  
Opened Hibernating_filtsharp.mrc as #3, grid size 270,270,270, pixel 2.59,
shown at level 0.00507, step 1, values float32  
Opened Int_Post_filtsharp.mrc as #4, grid size 270,270,270, pixel 2.59, shown
at level 0.00705, step 1, values float32  
Opened Post_filtsharp.mrc as #5, grid size 270,270,270, pixel 2.59, shown at
level 0.00678, step 1, values float32  
Opened Rotated_filtlocal.mrc as #6, grid size 270,270,270, pixel 2.59, shown
at level 0.00572, step 1, values float32  
Opened Translocating_filtsharp.mrc as #7, grid size 270,270,270, pixel 2.59,
shown at level 0.00737, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc as #8, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_none_filtsharp.mrc as #9, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened Hibernating_filtsharp.mrc 0 as #20.1, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 1 as #20.2, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 2 as #20.3, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 3 as #20.4, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 4 as #20.5, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 5 as #20.6, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Int_Post_filtsharp.mrc 0 as #19.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 1 as #19.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 2 as #19.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 3 as #19.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 4 as #19.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 5 as #19.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Post_filtsharp.mrc 0 as #21.1, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Post_filtsharp.mrc 1 as #21.2, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Post_filtsharp.mrc 2 as #21.3, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Post_filtsharp.mrc 3 as #21.4, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Rotated_filtlocal.mrc 0 as #22.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 1 as #22.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 2 as #22.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 3 as #22.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 4 as #22.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Translocating_filtsharp.mrc 0 as #23.1, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 1 as #23.2, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 2 as #23.3, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 3 as #23.4, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 4 as #23.5, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 5 as #23.6, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 0 as #24.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 1 as #24.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 2 as #24.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 3 as #24.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 4 as #24.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 5 as #24.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 6 as #24.7, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 0 as #25.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 1 as #25.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 2 as #25.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 3 as #25.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 4 as #25.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 5 as #25.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened Decoding_filtsharp.mrc 0 as #26.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 1 as #26.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 2 as #26.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 3 as #26.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 4 as #26.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 5 as #26.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 6 as #26.7, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 0 as #18.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 1 as #18.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 2 as #18.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 3 as #18.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 4 as #18.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 5 as #18.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened Rotated_filt.mrc as #10, grid size 270,270,270, pixel 2.59, shown at
level 0.00669, step 1, values float32  
Opened Rotated_filt.mrc 0 as #27.1, grid size 270,270,270, pixel 2.59, shown
at level 0.00669, step 1, values float32  
Opened Rotated_filt.mrc 1 as #27.2, grid size 270,270,270, pixel 2.59, shown
at level 0.00669, step 1, values float32  
Opened Rotated_filt.mrc 2 as #27.3, grid size 270,270,270, pixel 2.59, shown
at level 0.00669, step 1, values float32  
Opened Rotated_filt.mrc 3 as #27.4, grid size 270,270,270, pixel 2.59, shown
at level 0.00669, step 1, values float32  
Opened Rotated_filt.mrc 4 as #27.5, grid size 270,270,270, pixel 2.59, shown
at level 0.00669, step 1, values float32  

Not registering illegal selector name "40S"  

Log from Fri Feb 20 14:46:45 2026UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/20260217_FinaldensitiesWIP.cxs

Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 0 as #11.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 1 as #11.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 2 as #11.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 3 as #11.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 4 as #11.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 0 as #12.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 1 as #12.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 2 as #12.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 3 as #12.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 4 as #12.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 5 as #12.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 6 as #12.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 0 as #13.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 1 as #13.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 2 as #13.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 3 as #13.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 0 as #14.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 1 as #14.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 2 as #14.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 3 as #14.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 4 as #14.5, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 0 as #15.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 1 as #15.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 2 as #15.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 3 as #15.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 4 as #15.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 5 as #15.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 6 as #15.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 0 as #16.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 1 as #16.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 2 as #16.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 3 as #16.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 4 as #16.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 5 as #16.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 6 as #16.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 0 as #17.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 1 as #17.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 2 as #17.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 3 as #17.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 4 as #17.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 5 as #17.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened 60S_filtsharp.mrc as #1, grid size 270,270,270, pixel 2.59, shown at
level 0.00474, step 1, values float32  
Opened Decoding_filtsharp.mrc as #2, grid size 270,270,270, pixel 2.59, shown
at level 0.00591, step 1, values float32  
Opened Hibernating_filtsharp.mrc as #3, grid size 270,270,270, pixel 2.59,
shown at level 0.00507, step 1, values float32  
Opened Int_Post_filtsharp.mrc as #4, grid size 270,270,270, pixel 2.59, shown
at level 0.00705, step 1, values float32  
Opened Post_filtsharp.mrc as #5, grid size 270,270,270, pixel 2.59, shown at
level 0.00678, step 1, values float32  
Opened Rotated_filtlocal.mrc as #6, grid size 270,270,270, pixel 2.59, shown
at level 0.00572, step 1, values float32  
Opened Translocating_filtsharp.mrc as #7, grid size 270,270,270, pixel 2.59,
shown at level 0.00737, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc as #8, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_none_filtsharp.mrc as #9, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened Hibernating_filtsharp.mrc 0 as #20.1, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 1 as #20.2, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 2 as #20.3, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 3 as #20.4, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 4 as #20.5, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 5 as #20.6, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Int_Post_filtsharp.mrc 0 as #19.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 1 as #19.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 2 as #19.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 3 as #19.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 4 as #19.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 5 as #19.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Post_filtsharp.mrc 0 as #21.1, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Post_filtsharp.mrc 1 as #21.2, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Post_filtsharp.mrc 2 as #21.3, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Post_filtsharp.mrc 3 as #21.4, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Rotated_filtlocal.mrc 0 as #22.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 1 as #22.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 2 as #22.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 3 as #22.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 4 as #22.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Translocating_filtsharp.mrc 0 as #23.1, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 1 as #23.2, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 2 as #23.3, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 3 as #23.4, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 4 as #23.5, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 5 as #23.6, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 0 as #24.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 1 as #24.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 2 as #24.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 3 as #24.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 4 as #24.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 5 as #24.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 6 as #24.7, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 0 as #25.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 1 as #25.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 2 as #25.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 3 as #25.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 4 as #25.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 5 as #25.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened Decoding_filtsharp.mrc 0 as #26.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 1 as #26.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 2 as #26.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 3 as #26.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 4 as #26.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 5 as #26.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 6 as #26.7, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 0 as #18.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 1 as #18.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 2 as #18.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 3 as #18.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 4 as #18.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 5 as #18.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

Not registering illegal selector name "40S"  

Log from Fri Feb 20 10:54:41 2026UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/20260217_FinaldensitiesWIP.cxs
> format session

Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 0 as #10.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 1 as #10.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 2 as #10.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 3 as #10.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 4 as #10.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 5 as #10.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 0 as #11.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 1 as #11.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 2 as #11.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 3 as #11.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 4 as #11.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 0 as #12.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 1 as #12.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 2 as #12.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 3 as #12.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 4 as #12.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 5 as #12.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 6 as #12.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 0 as #13.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 1 as #13.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 2 as #13.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 3 as #13.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 0 as #14.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 1 as #14.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 2 as #14.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 3 as #14.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 4 as #14.5, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 0 as #15.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 1 as #15.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 2 as #15.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 3 as #15.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 4 as #15.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 5 as #15.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 6 as #15.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 0 as #16.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 1 as #16.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 2 as #16.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 3 as #16.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 4 as #16.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 5 as #16.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 6 as #16.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 0 as #17.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 1 as #17.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 2 as #17.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 3 as #17.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 4 as #17.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 5 as #17.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened 60S_filtsharp.mrc as #1, grid size 270,270,270, pixel 2.59, shown at
level 0.00474, step 1, values float32  
Opened Decoding_filtsharp.mrc as #2, grid size 270,270,270, pixel 2.59, shown
at level 0.00591, step 1, values float32  
Opened Hibernating_filtsharp.mrc as #3, grid size 270,270,270, pixel 2.59,
shown at level 0.00507, step 1, values float32  
Opened Int_Post_filtsharp.mrc as #4, grid size 270,270,270, pixel 2.59, shown
at level 0.00705, step 1, values float32  
Opened Post_filtsharp.mrc as #5, grid size 270,270,270, pixel 2.59, shown at
level 0.00678, step 1, values float32  
Opened Rotated_filtlocal.mrc as #6, grid size 270,270,270, pixel 2.59, shown
at level 0.00572, step 1, values float32  
Opened Translocating_filtsharp.mrc as #7, grid size 270,270,270, pixel 2.59,
shown at level 0.00737, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc as #8, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_none_filtsharp.mrc as #9, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened Decoding_filtsharp.mrc 0 as #18.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 1 as #18.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 2 as #18.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 3 as #18.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 4 as #18.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 5 as #18.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 6 as #18.7, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Hibernating_filtsharp.mrc 0 as #20.1, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 1 as #20.2, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 2 as #20.3, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 3 as #20.4, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 4 as #20.5, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 5 as #20.6, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Int_Post_filtsharp.mrc 0 as #19.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 1 as #19.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 2 as #19.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 3 as #19.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 4 as #19.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 5 as #19.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Post_filtsharp.mrc 0 as #21.1, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Post_filtsharp.mrc 1 as #21.2, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Post_filtsharp.mrc 2 as #21.3, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Post_filtsharp.mrc 3 as #21.4, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Rotated_filtlocal.mrc 0 as #22.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 1 as #22.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 2 as #22.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 3 as #22.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 4 as #22.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Translocating_filtsharp.mrc 0 as #23.1, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 1 as #23.2, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 2 as #23.3, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 3 as #23.4, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 4 as #23.5, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 5 as #23.6, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 0 as #24.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 1 as #24.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 2 as #24.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 3 as #24.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 4 as #24.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 5 as #24.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 6 as #24.7, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 0 as #25.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 1 as #25.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 2 as #25.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 3 as #25.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 4 as #25.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 5 as #25.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened LocRes_Bfac_-300_locres_filtered.mrc as #26, grid size 270,270,270,
pixel 2.59, shown at level 0.0132, step 2, values float32  

Not registering illegal selector name "40S"  

Log from Tue Feb 17 16:29:23 2026UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/PlaceholderDensitiesColoured.cxs

Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_60S.mrc as #1, grid size 128,128,128, pixel 4,
shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc as #2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc as #3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc as #4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc as #5, grid size 128,128,128, pixel
4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc as #6, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc as #7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc as #8, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc as #9, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 0 as #10.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 1 as #10.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 2 as #10.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 3 as #10.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 4 as #10.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 5 as #10.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 0 as #11.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 1 as #11.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 2 as #11.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 3 as #11.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 4 as #11.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 0 as #12.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 1 as #12.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 2 as #12.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 3 as #12.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 4 as #12.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 5 as #12.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 6 as #12.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 0 as #13.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 1 as #13.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 2 as #13.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 3 as #13.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 0 as #14.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 1 as #14.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 2 as #14.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 3 as #14.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 4 as #14.5, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 0 as #15.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 1 as #15.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 2 as #15.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 3 as #15.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 4 as #15.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 5 as #15.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 6 as #15.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 0 as #16.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 1 as #16.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 2 as #16.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 3 as #16.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 4 as #16.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 5 as #16.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 6 as #16.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 0 as #17.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 1 as #17.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 2 as #17.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 3 as #17.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 4 as #17.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 5 as #17.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

Not registering illegal selector name "40S"  

Log from Mon Feb 9 13:25:44 2026UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/Manuscript1/Ribofigs/PlaceholderDensitiesColoured.cxs

Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_60S.mrc as #1, grid size 128,128,128, pixel 4,
shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc as #2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc as #3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc as #4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc as #5, grid size 128,128,128, pixel
4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc as #6, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc as #7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc as #8, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc as #9, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 0 as #10.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 1 as #10.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 2 as #10.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 3 as #10.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 4 as #10.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 5 as #10.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 0 as #11.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 1 as #11.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 2 as #11.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 3 as #11.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 4 as #11.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 0 as #12.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 1 as #12.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 2 as #12.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 3 as #12.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 4 as #12.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 5 as #12.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 6 as #12.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 0 as #13.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 1 as #13.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 2 as #13.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 3 as #13.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 0 as #14.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 1 as #14.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 2 as #14.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 3 as #14.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 4 as #14.5, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 0 as #15.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 1 as #15.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 2 as #15.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 3 as #15.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 4 as #15.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 5 as #15.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 6 as #15.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 0 as #16.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 1 as #16.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 2 as #16.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 3 as #16.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 4 as #16.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 5 as #16.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 6 as #16.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 0 as #17.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 1 as #17.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 2 as #17.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 3 as #17.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 4 as #17.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 5 as #17.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

Not registering illegal selector name "40S"  

Log from Wed Feb 4 17:42:03 2026UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/Manuscript1/Ribofigs/202602_subunitcolouring.cxs

Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.7, step 1, values float32  

Not registering illegal selector name "40S"  

Log from Wed Feb 4 15:33:49 2026UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/Manuscript1/202512_subunitcolouring.cxs

Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc as #1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc as #2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc as #3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc as #4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc as #5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc as #6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc as #7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc as #8, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc as #9, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc as #10, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc as #11, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_open.mrc as #12, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc as #13, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc as #14, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc as #15, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc as #16, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc as #17, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc as #18, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc as #19, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 0 as #20.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 1 as #20.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 2 as #20.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 3 as #20.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 4 as #20.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 5 as #20.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 6 as #20.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 0 as #21.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 1 as #21.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 2 as #21.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 3 as #21.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 4 as #21.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 5 as #21.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 6 as #21.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 0 as #22.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 1 as #22.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 2 as #22.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 3 as #22.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 4 as #22.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 5 as #22.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 0 as #23.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 1 as #23.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 2 as #23.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 3 as #23.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 4 as #23.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 5 as #23.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 6 as #23.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 0 as #24.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 1 as #24.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 2 as #24.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 3 as #24.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 4 as #24.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 5 as #24.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 6 as #24.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 0 as #25.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 1 as #25.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 2 as #25.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 3 as #25.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 4 as #25.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 5 as #25.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 0 as #26.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 1 as #26.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 2 as #26.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 3 as #26.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 4 as #26.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 0 as #27.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 1 as #27.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 2 as #27.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 3 as #27.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 4 as #27.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc 0 as #28.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc 1 as #28.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc 2 as #28.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc 3 as #28.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 0 as #29.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 1 as #29.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 2 as #29.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 3 as #29.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 4 as #29.5, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc 0 as #30.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc 1 as #30.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc 2 as #30.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc 3 as #30.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc 4 as #30.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_open.mrc 0 as #31.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_open.mrc 1 as #31.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_open.mrc 2 as #31.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_open.mrc 3 as #31.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 0 as #32.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 1 as #32.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 2 as #32.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 3 as #32.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 4 as #32.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 0 as #34.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 1 as #34.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 2 as #34.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 3 as #34.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 4 as #34.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 5 as #34.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 6 as #34.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 0 as #35.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 1 as #35.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 2 as #35.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 3 as #35.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 4 as #35.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 5 as #35.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 6 as #35.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 0 as #36.1, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 1 as #36.2, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 2 as #36.3, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 3 as #36.4, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 4 as #36.5, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 5 as #36.6, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 0 as #37.1, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 1 as #37.2, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 2 as #37.3, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 3 as #37.4, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 4 as #37.5, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 5 as #37.6, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 6 as #37.7, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 0 as #38.1, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 1 as #38.2, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 2 as #38.3, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 3 as #38.4, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 4 as #38.5, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 5 as #38.6, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 0 as #33.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 1 as #33.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 2 as #33.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 3 as #33.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 4 as #33.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 5 as #33.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

Not registering illegal selector name "40S"  

Log from Wed Jan 7 10:53:50 2026UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/Manuscript1/202512_subunitcolouring.cxs

Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc as #1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc as #2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc as #3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc as #4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc as #5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc as #6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc as #7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc as #8, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc as #9, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc as #10, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc as #11, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_open.mrc as #12, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc as #13, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc as #14, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc as #15, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc as #16, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc as #17, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc as #18, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc as #19, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 0 as #20.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 1 as #20.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 2 as #20.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 3 as #20.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 4 as #20.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 5 as #20.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 6 as #20.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 0 as #21.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 1 as #21.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 2 as #21.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 3 as #21.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 4 as #21.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 5 as #21.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 6 as #21.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 0 as #22.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 1 as #22.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 2 as #22.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 3 as #22.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 4 as #22.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 5 as #22.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 0 as #23.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 1 as #23.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 2 as #23.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 3 as #23.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 4 as #23.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 5 as #23.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 6 as #23.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 0 as #24.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 1 as #24.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 2 as #24.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 3 as #24.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 4 as #24.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 5 as #24.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 6 as #24.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 0 as #25.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 1 as #25.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 2 as #25.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 3 as #25.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 4 as #25.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 5 as #25.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 0 as #26.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 1 as #26.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 2 as #26.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 3 as #26.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 4 as #26.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 0 as #27.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 1 as #27.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 2 as #27.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 3 as #27.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 4 as #27.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc 0 as #28.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc 1 as #28.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc 2 as #28.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc 3 as #28.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 0 as #29.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 1 as #29.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 2 as #29.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 3 as #29.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 4 as #29.5, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc 0 as #30.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc 1 as #30.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc 2 as #30.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc 3 as #30.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc 4 as #30.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_open.mrc 0 as #31.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_open.mrc 1 as #31.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_open.mrc 2 as #31.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_open.mrc 3 as #31.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 0 as #32.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 1 as #32.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 2 as #32.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 3 as #32.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 4 as #32.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 0 as #33.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 1 as #33.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 2 as #33.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 3 as #33.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 4 as #33.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 5 as #33.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 6 as #33.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 0 as #34.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 1 as #34.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 2 as #34.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 3 as #34.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 4 as #34.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 5 as #34.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 6 as #34.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 0 as #35.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 1 as #35.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 2 as #35.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 3 as #35.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 4 as #35.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 5 as #35.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 6 as #35.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 0 as #36.1, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 1 as #36.2, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 2 as #36.3, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 3 as #36.4, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 4 as #36.5, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 5 as #36.6, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 0 as #37.1, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 1 as #37.2, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 2 as #37.3, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 3 as #37.4, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 4 as #37.5, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 5 as #37.6, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 6 as #37.7, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 0 as #38.1, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 1 as #38.2, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 2 as #38.3, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 3 as #38.4, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 4 as #38.5, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 5 as #38.6, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

Not registering illegal selector name "40S"  

Log from Wed Dec 17 16:42:20 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/Manuscript1/202512_subunitcolouring.cxs

Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc as #8, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc as #9, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc as #10, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc as #11, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc as #12, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc as #13, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc as #14, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 0 as #1.1, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 1 as #1.2, grid size
128,128,128, pixel 4, shown at level 0.708, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 2 as #1.3, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 3 as #1.4, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 4 as #1.5, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 5 as #1.6, grid size
128,128,128, pixel 4, shown at level 0.614, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 6 as #1.7, grid size
128,128,128, pixel 4, shown at level 0.527, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 0 as #2.1, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 1 as #2.2, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 2 as #2.3, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 3 as #2.4, grid size
128,128,128, pixel 4, shown at level 0.605, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 4 as #2.5, grid size
128,128,128, pixel 4, shown at level 0.599, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 0 as #3.1, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 1 as #3.2, grid size 128,128,128,
pixel 4, shown at level 0.608, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 2 as #3.3, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 3 as #3.4, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 4 as #3.5, grid size 128,128,128,
pixel 4, shown at level 0.599, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 0 as #5.1, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 1 as #5.2, grid size 128,128,128,
pixel 4, shown at level 0.61, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 2 as #5.3, grid size 128,128,128,
pixel 4, shown at level 0.644, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 3 as #5.4, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 4 as #5.5, grid size 128,128,128,
pixel 4, shown at level 0.607, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 5 as #5.6, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 0 as #6.1, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 1 as #6.2, grid size
128,128,128, pixel 4, shown at level 0.632, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 2 as #6.3, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 3 as #6.4, grid size
128,128,128, pixel 4, shown at level 0.605, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 4 as #6.5, grid size
128,128,128, pixel 4, shown at level 0.616, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 5 as #6.6, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 0 as #7.1, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 1 as #7.2, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 2 as #7.3, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 3 as #7.4, grid size
128,128,128, pixel 4, shown at level 0.66, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 4 as #7.5, grid size
128,128,128, pixel 4, shown at level 0.569, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 5 as #7.6, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 6 as #7.7, grid size
128,128,128, pixel 4, shown at level 0.62, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 0 as #4.1, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 1 as #4.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 2 as #4.3, grid size 128,128,128,
pixel 4, shown at level 0.578, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 3 as #4.4, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 4 as #4.5, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  

Not registering illegal selector name "40S"  

Log from Tue Aug 12 16:48:18 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/202508_subunitcolouring.cxs

Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.65, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc as #8, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc as #9, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc as #10, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc as #11, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc as #12, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc as #13, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc as #14, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

Not registering illegal selector name "40S"  

Log from Tue Aug 12 16:26:11 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/subunit_colouring2.cxs

Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.65, step 1, values float32  
Opened 160_decodingE.mrc as #1, grid size 128,128,128, pixel 4, shown at level
0.6, step 1, values float32  
Opened 160_hibernatingE.mrc as #2, grid size 128,128,128, pixel 4, shown at
level 0.6, step 1, values float32  
Opened 160_Post?.mrc as #3, grid size 128,128,128, pixel 4, shown at level
0.6, step 1, values float32  
Opened 160_unr_pre5.mrc as #4, grid size 128,128,128, pixel 4, shown at level
0.6, step 1, values float32  
Opened 160_hibernating5 as #5, grid size 128,128,128, pixel 4, shown at level
0.6, step 1, values float32  
Opened 160_rot as #6, grid size 128,128,128, pixel 4, shown at level 0.6, step
1, values float32  
Opened 160_decoding5 as #7, grid size 128,128,128, pixel 4, shown at level
0.6, step 1, values float32  

Not registering illegal selector name "40S"  

Log from Wed Jan 15 14:45:55 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/subunit_colouring.cxs

Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.65, step 1, values float32  
Opened MultiPostProcessor_PPout_9.mrc as #1, grid size 128,128,128, pixel 4,
shown at level 0.65, step 1, values float32  
Opened MultiPostProcessor_PPout_3.mrc as #3, grid size 128,128,128, pixel 4,
shown at level 0.65, step 1, values float32  
Opened MultiPostProcessor_PPout_6.mrc as #4, grid size 128,128,128, pixel 4,
shown at level 0.65, step 1, values float32  
Opened MultiPostProcessor_PPout_7.mrc as #5, grid size 128,128,128, pixel 4,
shown at level 0.65, step 1, values float32  

Not registering illegal selector name "40S"  

Log from Tue Sep 24 13:28:01 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/subunit_colouring.cxs

Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_9.mrc as #1, grid size 128,128,128, pixel 4,
shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_3.mrc as #3, grid size 128,128,128, pixel 4,
shown at level 0.65, step 1, values float32  
Opened MultiPostProcessor_PPout_6.mrc as #4, grid size 128,128,128, pixel 4,
shown at level 0.65, step 1, values float32  
Opened MultiPostProcessor_PPout_7.mrc as #5, grid size 128,128,128, pixel 4,
shown at level 0.65, step 1, values float32  

Not registering illegal selector name "40S"  

Log from Thu Sep 12 05:33:16 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/campbell/Desktop/Chimera_sessions/subunit_colouring.cxs

Opened EMD-12059_PRE1.mrc as #51, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12061_PRE2.mrc as #52, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12075_PRE3.mrc as #53, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12065_PRE4.mrc as #54, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12074_POST1.mrc as #55, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12062_POST2.mrc as #56, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12064_POST3.mrc as #57, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_9.mrc as #1, grid size 128,128,128, pixel 4,
shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_9.mrc 0 as #2.1, grid size 128,128,128, pixel
4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_9.mrc 1 as #2.2, grid size 128,128,128, pixel
4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_9.mrc 2 as #2.3, grid size 128,128,128, pixel
4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_9.mrc 3 as #2.4, grid size 128,128,128, pixel
4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_9.mrc 4 as #2.5, grid size 128,128,128, pixel
4, shown at level 0.7, step 1, values float32  

Not registering illegal selector name "40S"  

Log from Wed Sep 11 21:36:06 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/Conformationassignment/RotationPDBsandEMDBsCombined.cxs

Opened EMD-12059_PRE1.mrc as #51, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12061_PRE2.mrc as #52, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12075_PRE3.mrc as #53, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12065_PRE4.mrc as #54, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12074_POST1.mrc as #55, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12062_POST2.mrc as #56, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12064_POST3.mrc as #57, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.6, step 1, values float32  
Log from Fri Aug 9 12:43:00 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/Conformationassignment/RotationPDBsandEMDBsCombined.cxs

Opened EMD-12059_PRE1.mrc as #51, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12061_PRE2.mrc as #52, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12075_PRE3.mrc as #53, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12065_PRE4.mrc as #54, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12074_POST1.mrc as #55, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12062_POST2.mrc as #56, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened EMD-12064_POST3.mrc as #57, grid size 420,420,420, pixel 1.08, shown at
level 0.03, step 2, values float32  
Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.785, step 1, values float32  
Log from Thu Aug 8 16:15:28 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/Conformationassignment/RotationPDBsandEMDBsCombined.cxs

Opened EMD-12059_PRE1.mrc as #51, grid size 420,420,420, pixel 1.08, shown at
level 0.0451, step 2, values float32  
Opened EMD-12061_PRE2.mrc as #52, grid size 420,420,420, pixel 1.08, shown at
level 0.0416, step 2, values float32  
Opened EMD-12075_PRE3.mrc as #53, grid size 420,420,420, pixel 1.08, shown at
level 0.04, step 2, values float32  
Opened EMD-12065_PRE4.mrc as #54, grid size 420,420,420, pixel 1.08, shown at
level 0.0481, step 2, values float32  
Opened EMD-12074_POST1.mrc as #55, grid size 420,420,420, pixel 1.08, shown at
level 0.038, step 2, values float32  
Opened EMD-12062_POST2.mrc as #56, grid size 420,420,420, pixel 1.08, shown at
level 0.0447, step 2, values float32  
Opened EMD-12064_POST3.mrc as #57, grid size 420,420,420, pixel 1.08, shown at
level 0.0444, step 2, values float32  
Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.785, step 1, values float32  
Log from Thu Aug 8 13:05:51 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/campbell/Desktop/Chimera_sessions/Conformationassignment/RotationPDBsandEMDBsCombined.cxs

Opened EMD-12059_PRE1.mrc as #51, grid size 420,420,420, pixel 1.08, shown at
level 0.0451, step 2, values float32  
Opened EMD-12061_PRE2.mrc as #52, grid size 420,420,420, pixel 1.08, shown at
level 0.0416, step 2, values float32  
Opened EMD-12075_PRE3.mrc as #53, grid size 420,420,420, pixel 1.08, shown at
level 0.04, step 2, values float32  
Opened EMD-12065_PRE4.mrc as #54, grid size 420,420,420, pixel 1.08, shown at
level 0.0481, step 2, values float32  
Opened EMD-12074_POST1.mrc as #55, grid size 420,420,420, pixel 1.08, shown at
level 0.038, step 2, values float32  
Opened EMD-12062_POST2.mrc as #56, grid size 420,420,420, pixel 1.08, shown at
level 0.0447, step 2, values float32  
Opened EMD-12064_POST3.mrc as #57, grid size 420,420,420, pixel 1.08, shown at
level 0.0444, step 2, values float32  
Opened Stable_60S.mrc as #50, grid size 128,128,128, pixel 4, shown at level
0.785, step 1, values float32  
Log from Thu Aug 8 12:51:05 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/campbell/Desktop/Chimera_sessions/Conformationassignment/Stable_60S.mrc

Opened Stable_60S.mrc as #1, grid size 128,128,128, pixel 4, shown at level
0.818, step 1, values float32  

> volume #1 level 0.7854

> open 3j78

3j78 title:  
Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated
conformations (Class I - non-rotated ribosome with 2 tRNAs) [more info...]  
  
Chain information for 3j78 #2  
---  
Chain | Description | UniProt  
10 | 40S ribosomal protein S10 | RS10A_YEAST 1-105  
11 | 40S ribosomal protein S11 | RS11A_YEAST 1-156  
12 | 40S ribosomal protein S12 | RS12_YEAST 1-143  
13 | 40S ribosomal protein S13 | RS13_YEAST 1-151  
14 | 40S ribosomal protein S14 | RS14A_YEAST 1-137  
15 | 40S ribosomal protein S15 | RS15_YEAST 1-142  
16 | 40S ribosomal protein S16 | RS16A_YEAST 1-143  
17 | 40S ribosomal protein S17 | RS17A_YEAST 1-136  
18 | 40S ribosomal protein S18 | RS18A_YEAST 1-146  
19 | 40S ribosomal protein S19 | RS19A_YEAST 1-144  
1S | 18S ribosomal RNA |   
20 | 40S ribosomal protein S20 | RS20_YEAST 1-121  
21 | 40S ribosomal protein S21 | RS21A_YEAST 1-87  
22 | 40S ribosomal protein S22 | RS22A_YEAST 1-130  
23 | 40S ribosomal protein S23 | RS23A_YEAST 1-145  
24 | 40S ribosomal protein S24 | RS24A_YEAST 1-135  
25 | 40S ribosomal protein S25 | RS25A_YEAST 1-108  
26 | 40S ribosomal protein S26 | RS26A_YEAST 1-119  
27 | 40S ribosomal protein S27 | RS27_YEAST 1-82  
28 | 40S ribosomal protein S28 | RS28A_YEAST 1-67  
29 | 40S ribosomal protein S29 | RS29A_YEAST 1-56  
2S | 25S ribosomal RNA |   
30 | 40S ribosomal protein S30 | RS30A_YEAST 1-63  
31 | 40S ribosomal protein S31 | RS27A_YEAST 1-152  
5S | 5S ribosomal RNA |   
60 | 60S ribosomal protein L10 | RL10_YEAST 1-221  
61 | 60S ribosomal protein L11 | RL11A_YEAST 1-174  
62 | 60S ribosomal protein L12 | RL12A_YEAST 1-165  
63 | 60S ribosomal protein L13 | RL13A_YEAST 1-199  
64 | 60S ribosomal protein L14 | RL14A_YEAST 1-138  
65 | 60S ribosomal protein L15 | RL15A_YEAST 1-204  
66 | 60S ribosomal protein L16 | RL16A_YEAST 1-199  
67 | 60S ribosomal protein L17 | RL17A_YEAST 1-184  
68 | 60S ribosomal protein L18 | RL18A_YEAST 1-186  
69 | 60S ribosomal protein L19 | RL19A_YEAST 1-189  
70 | 60S ribosomal protein L20 | RL20A_YEAST 1-172  
71 | 60S ribosomal protein L21 | RL21A_YEAST 1-160  
72 | 60S ribosomal protein L22 | RL22A_YEAST 1-121  
73 | 60S ribosomal protein L23 | RL23A_YEAST 1-137  
74 | 60S ribosomal protein L24 | RL24A_YEAST 1-155  
75 | 60S ribosomal protein L25 | RL25_YEAST 1-142  
76 | 60S ribosomal protein L26 | RL26A_YEAST 1-127  
77 | 60S ribosomal protein L27 | RL27A_YEAST 1-136  
78 | 60S ribosomal protein L28 | RL28_YEAST 1-149  
79 | 60S ribosomal protein L29 | RL29_YEAST 1-59  
80 | 60S ribosomal protein L30 | RL30_YEAST 1-105  
81 | 60S ribosomal protein L31 | RL31A_YEAST 1-113  
82 | 60S ribosomal protein L32 | RL32_YEAST 1-130  
83 | 60S ribosomal protein L33 | RL33A_YEAST 1-107  
84 | 60S ribosomal protein L34 | RL34A_YEAST 1-121  
85 | 60S ribosomal protein L35 | RL35A_YEAST 1-120  
86 | 60S ribosomal protein L36 | RL36A_YEAST 1-100  
87 | 60S ribosomal protein L37 | RL37A_YEAST 1-88  
88 | 60S ribosomal protein L38 | RL38_YEAST 1-78  
89 | 60S ribosomal protein L39 | RL39_YEAST 1-51  
8S | 5.8S ribosomal RNA |   
90 | 60S ribosomal protein L40 | RL401_YEAST 1-128  
91 | 60S ribosomal protein L41 | RL41A_YEAST 1-25  
92 | 60S ribosomal protein L42 | RL44A_YEAST 1-106  
93 | 60S ribosomal protein L43 | RL43A_YEAST 1-92  
ET PT | P/E-site initiator transfer RNAfMet |   
L1 | 60S ribosomal protein L1 | RL1A_YEAST 1-217  
L2 | 60S ribosomal protein L2 | RL2A_YEAST 1-254  
L3 | 60S ribosomal protein L3 | RL3_YEAST 1-387  
L4 | 60S ribosomal protein L4 | RL4A_YEAST 1-362  
L5 | 60S ribosomal protein L5 | RL5_YEAST 1-297  
L6 | 60S ribosomal protein L6 | RL6A_YEAST 1-176  
L7 | 60S ribosomal protein L7 | RL7A_YEAST 1-244  
L8 | 60S ribosomal protein L8 | RL8A_YEAST 1-256  
L9 | 60S ribosomal protein L9 | RL9A_YEAST 1-191  
MR | messenger RNA |   
P0 | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-312  
RC | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 1-319  
S0 | 40S ribosomal protein S0 | RSSA1_YEAST 1-252  
S1 | 40S ribosomal protein S1 | RS3A1_YEAST 1-255  
S2 | 40S ribosomal protein S2 | RS2_YEAST 1-254  
S3 | 40S ribosomal protein S3 | RS3_YEAST 1-240  
S4 | 40S ribosomal protein S4 | RS4A_YEAST 1-261  
S5 | 40S ribosomal protein S5 | RS5_YEAST 1-225  
S6 | 40S ribosomal protein S6 | RS6A_YEAST 1-236  
S7 | 40S ribosomal protein S7 | RS7A_YEAST 1-190  
S8 | 40S ribosomal protein S8 | RS8A_YEAST 1-200  
S9 | 40S ribosomal protein S9 | RS9A_YEAST 1-197  
  

> open 3j77

3j77 title:  
Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated
conformations (Class II - rotated ribosome with 1 tRNA) [more info...]  
  
Chain information for 3j77 #3  
---  
Chain | Description | UniProt  
10 | 40S ribosomal protein S10 | RS10A_YEAST 1-105  
11 | 40S ribosomal protein S11 | RS11A_YEAST 1-156  
12 | 40S ribosomal protein S12 | RS12_YEAST 1-143  
13 | 40S ribosomal protein S13 | RS13_YEAST 1-151  
14 | 40S ribosomal protein S14 | RS14A_YEAST 1-137  
15 | 40S ribosomal protein S15 | RS15_YEAST 1-142  
16 | 40S ribosomal protein S16 | RS16A_YEAST 1-143  
17 | 40S ribosomal protein S17 | RS17A_YEAST 1-136  
18 | 40S ribosomal protein S18 | RS18A_YEAST 1-146  
19 | 40S ribosomal protein S19 | RS19A_YEAST 1-144  
1S | 18S ribosomal RNA |   
20 | 40S ribosomal protein S20 | RS20_YEAST 1-121  
21 | 40S ribosomal protein S21 | RS21A_YEAST 1-87  
22 | 40S ribosomal protein S22 | RS22A_YEAST 1-130  
23 | 40S ribosomal protein S23 | RS23A_YEAST 1-145  
24 | 40S ribosomal protein S24 | RS24A_YEAST 1-135  
25 | 40S ribosomal protein S25 | RS25A_YEAST 1-108  
26 | 40S ribosomal protein S26 | RS26A_YEAST 1-119  
27 | 40S ribosomal protein S27 | RS27_YEAST 1-82  
28 | 40S ribosomal protein S28 | RS28A_YEAST 1-67  
29 | 40S ribosomal protein S29 | RS29A_YEAST 1-56  
2S | 25S ribosomal RNA |   
30 | 40S ribosomal protein S30 | RS30A_YEAST 1-63  
31 | 40S ribosomal protein S31 | RS27A_YEAST 1-152  
5S | 5S ribosomal RNA |   
60 | 60S ribosomal protein L10 | RL10_YEAST 1-221  
61 | 60S ribosomal protein L11 | RL11A_YEAST 1-174  
62 | 60S ribosomal protein L12 | RL12A_YEAST 1-165  
63 | 60S ribosomal protein L13 | RL13A_YEAST 1-199  
64 | 60S ribosomal protein L14 | RL14A_YEAST 1-138  
65 | 60S ribosomal protein L15 | RL15A_YEAST 1-204  
66 | 60S ribosomal protein L16 | RL16A_YEAST 1-199  
67 | 60S ribosomal protein L17 | RL17A_YEAST 1-184  
68 | 60S ribosomal protein L18 | RL18A_YEAST 1-186  
69 | 60S ribosomal protein L19 | RL19A_YEAST 1-189  
70 | 60S ribosomal protein L20 | RL20A_YEAST 1-172  
71 | 60S ribosomal protein L21 | RL21A_YEAST 1-160  
72 | 60S ribosomal protein L22 | RL22A_YEAST 1-121  
73 | 60S ribosomal protein L23 | RL23A_YEAST 1-137  
74 | 60S ribosomal protein L24 | RL24A_YEAST 1-155  
75 | 60S ribosomal protein L25 | RL25_YEAST 1-142  
76 | 60S ribosomal protein L26 | RL26A_YEAST 1-127  
77 | 60S ribosomal protein L27 | RL27A_YEAST 1-136  
78 | 60S ribosomal protein L28 | RL28_YEAST 1-149  
79 | 60S ribosomal protein L29 | RL29_YEAST 1-59  
80 | 60S ribosomal protein L30 | RL30_YEAST 1-105  
81 | 60S ribosomal protein L31 | RL31A_YEAST 1-113  
82 | 60S ribosomal protein L32 | RL32_YEAST 1-130  
83 | 60S ribosomal protein L33 | RL33A_YEAST 1-107  
84 | 60S ribosomal protein L34 | RL34A_YEAST 1-121  
85 | 60S ribosomal protein L35 | RL35A_YEAST 1-120  
86 | 60S ribosomal protein L36 | RL36A_YEAST 1-100  
87 | 60S ribosomal protein L37 | RL37A_YEAST 1-88  
88 | 60S ribosomal protein L38 | RL38_YEAST 1-78  
89 | 60S ribosomal protein L39 | RL39_YEAST 1-51  
8S | 5.8S ribosomal RNA |   
90 | 60S ribosomal protein L40 | RL401_YEAST 1-128  
91 | 60S ribosomal protein L41 | RL41A_YEAST 1-25  
92 | 60S ribosomal protein L42 | RL44A_YEAST 1-106  
93 | 60S ribosomal protein L43 | RL43A_YEAST 1-92  
L1 | 60S ribosomal protein L1 | RL1A_YEAST 1-217  
L2 | 60S ribosomal protein L2 | RL2A_YEAST 1-254  
L3 | 60S ribosomal protein L3 | RL3_YEAST 1-387  
L4 | 60S ribosomal protein L4 | RL4A_YEAST 1-362  
L5 | 60S ribosomal protein L5 | RL5_YEAST 1-297  
L6 | 60S ribosomal protein L6 | RL6A_YEAST 1-176  
L7 | 60S ribosomal protein L7 | RL7A_YEAST 1-244  
L8 | 60S ribosomal protein L8 | RL8A_YEAST 1-256  
L9 | 60S ribosomal protein L9 | RL9A_YEAST 1-191  
MR | messenger RNA |   
P0 | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-312  
PT | P/E-site initiator transfer RNAfMet |   
RC | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 1-319  
S0 | 40S ribosomal protein S0 | RSSA1_YEAST 1-252  
S1 | 40S ribosomal protein S1 | RS3A1_YEAST 1-255  
S2 | 40S ribosomal protein S2 | RS2_YEAST 1-254  
S3 | 40S ribosomal protein S3 | RS3_YEAST 1-240  
S4 | 40S ribosomal protein S4 | RS4A_YEAST 1-261  
S5 | 40S ribosomal protein S5 | RS5_YEAST 1-225  
S6 | 40S ribosomal protein S6 | RS6A_YEAST 1-236  
S7 | 40S ribosomal protein S7 | RS7A_YEAST 1-190  
S8 | 40S ribosomal protein S8 | RS8A_YEAST 1-200  
S9 | 40S ribosomal protein S9 | RS9A_YEAST 1-197  
  

> open 7osm

7osm title:  
Intermediate translocation complex of 80 S.cerevisiae ribosome with eEF2 and
ligands [more info...]  
  
Chain information for 7osm #4  
---  
Chain | Description | UniProt  
18S | 18S rRNA |   
25S | 25S rRNA |   
58S | 5.8S rRNA |   
AB | 5S rRNA |   
ASIT | PHE tRNA |   
PSIT | FMET tRNA |   
RACK | BJ4_G0022010.mRNA.1.CDS.1 | A0A6L1BKH8_YEASX 1-319  
eEF2 | Elongation factor 2 | A0A6A5Q7K2_YEASX 1-842  
eL13 | 60S ribosomal protein L13 | A0A6L1AF71_YEASX 1-199  
eL14 | 60S ribosomal protein L14-A | RL14A_YEAST 1-138  
eL15 | 60S ribosomal protein L15-A | RL15A_YEAST 1-204  
eL18 | BJ4_G0033900.mRNA.1.CDS.1 | A0A6L1A7F6_YEASX 1-186  
eL19 | 60S ribosomal protein L19-A | RL19A_YEAST 1-189  
eL20 | 60S ribosomal protein L20 | A0A6V8RR03_YEASX 1-172  
eL21 | BJ4_G0003770.mRNA.1.CDS.1 | A0A6L0YTI6_YEASX 1-160  
eL22 | 60S ribosomal protein L22-A | A0A6L0ZZW6_YEASX 1-121  
eL24 | 60S ribosomal protein L24-A | A0A6A5PY83_YEASX 1-155  
eL27 | 60S ribosomal protein L27 | A0A6L0ZQQ7_YEASX 1-136  
eL29 | 60S ribosomal protein L29 | A0A6A5PWR1_YEASX 1-59  
eL30 | BJ4_G0020000.mRNA.1.CDS.1 | A0A6L0ZM08_YEASX 1-105  
eL31 | BJ4_G0008090.mRNA.1.CDS.1 | A0A6L0YFR2_YEASX 1-113  
eL32 | HN1_G0013350.mRNA.1.CDS.1 | A0A7I9CD28_YEASX 1-130  
eL33 | BJ4_G0025510.mRNA.1.CDS.1 | A0A6L1C3H0_YEASX 1-107  
eL34 | 60S ribosomal protein L34-A | A0A6L0ZFW3_YEASX 1-121  
eL36 | 60S ribosomal protein L36-A | RL36A_YEAST 1-100  
eL37 | Ribosomal protein L37 | A0A6L1BIE7_YEASX 1-88  
eL38 | BJ4_G0032190.mRNA.1.CDS.1 | A0A6A5PUL8_YEASX 1-78  
eL39 | 60S ribosomal protein L39 | A0A6L1ASX0_YEASX 1-51  
eL40 | Ubiquitin | A0A6V8S9K0_YEASX 1-128  
eL41 | eL41 |   
eL42 | BJ4_G0001880.mRNA.1.CDS.1 | A0A6L1B5X0_YEASX 1-106  
eL43 | 60S ribosomal protein L43-A | RL43A_YEAST 1-92  
eL6 | 60S ribosomal protein L6 | A0A6L1BLT3_YEASX 1-176  
eL8 | 60S ribosomal protein L8-A | RL8A_YEAST 1-256  
eS1 | 40S ribosomal protein S1 | A0A6A5PRY4_YEASX 1-255  
eS10 | 40S ribosomal protein S10-A | A0A6L0ZM59_YEASX 1-105  
eS17 | BJ4_G0020710.mRNA.1.CDS.1 | A0A6L1BLL7_YEASX 1-136  
eS19 | 40S ribosomal protein S19-A | A0A6L1BWT3_YEASX 1-144  
eS21 | 40S ribosomal protein S21 | A0A6L1BDN3_YEASX 1-87  
eS24 | 40S ribosomal protein S24 | A0A6L1AUB6_YEASX 1-135  
eS25 | 40S ribosomal protein S25 | A0A6A5PZ18_YEASX 1-108  
eS26 | 40S ribosomal protein S26 | A0A6A5PUG0_YEASX 1-119  
eS27 | 40S ribosomal protein S27-A | RS27A_YEAST 1-82  
eS28 | eS28 | A0A6A5Q700_YEASX 1-67  
eS30 | 40S ribosomal protein S30 | A0A6L1A1E1_YEASX 1-63  
eS31 | Ubiquitin-40S ribosomal protein S31 | A0A6A5PU37_YEASX 1-152  
eS4 | 40S ribosomal protein S4 | A0A6L0Z3Q0_YEASX 1-261  
eS6 | 40S ribosomal protein S6 | A0A6L1AMY1_YEASX 1-236  
eS7 | 40S ribosomal protein S7 | A0A6L1ACT7_YEASX 1-190  
eS8 | 40S ribosomal protein S8 | A0A6A5Q1H1_YEASX 1-200  
mRNA | MRNA |   
uL10 | 60S acidic ribosomal protein P0 | A0A6A5PT43_YEASX 1-312  
uL11 | 60S ribosomal protein L12-B | A0A6A5Q275_YEASX 1-165  
uL13 | 60S ribosomal protein L16-A | A0A6L0ZD57_YEASX 1-199  
uL14 | 60S ribosomal protein L23-B | A0A6L0Z7E4_YEASX 1-137  
uL15 | 60S ribosomal protein L28 | A0A6L0ZDK5_YEASX 1-149  
uL16 | 60S ribosomal protein L10 | A0A6A5PUZ5_YEASX 1-221  
uL18 | 60S ribosomal protein L5 | A0A6A5Q0W8_YEASX 1-297  
uL2 | 60S ribosomal protein L2-B | A0A6L0Y8L2_YEASX 1-254  
uL22 | BJ4_G0005750.mRNA.1.CDS.1 | A0A6L1BCL1_YEASX 1-184  
uL23 | 60S ribosomal protein L25 | A0A6L0YSM0_YEASX 1-142  
uL24 | 60S ribosomal protein L26-A | RL26A_YEAST 1-127  
uL29 | BJ4_G0044250.mRNA.1.CDS.1 | A0A7I9BRN0_YEASX 1-120  
uL3 | 60S ribosomal protein L3 | A0A6A5Q627_YEASX 1-387  
uL30 | 60S ribosomal protein L7-A | A0A6V8RJA7_YEASX 1-244  
uL4 | BJ4_G0008850.mRNA.1.CDS.1 | A0A6A5Q3W0_YEASX 1-362  
uL5 | BJ4_G0027750.mRNA.1.CDS.1 | A0A6A5Q7I9_YEASX 1-174  
uL6 | 60S ribosomal protein L9-A | RL9A_YEAST 1-191  
uS10 | 40S ribosomal protein S20 | A0A6A5PVE9_YEASX 1-121  
uS11 | 40S ribosomal protein S14-A | A0A6L1AAG7_YEASX 1-137  
uS12 | 40S ribosomal protein S23 | A0A6L1B1T2_YEASX 1-145  
uS13 | 40S ribosomal protein S18-B | A0A6L1AIT6_YEASX 1-146  
uS14 | HLJ1_G0030400.mRNA.1.CDS.1 | A0A6A5PV92_YEASX 1-56  
uS15 | 40S ribosomal protein S13 | A0A6L0YFM5_YEASX 1-151  
uS17 | 40S ribosomal protein S11-B | A0A6L0YMX6_YEASX 1-156  
uS19 | 40S ribosomal protein S15 | A0A6A5Q6F2_YEASX 1-142  
uS2 | 40S ribosomal protein S0 | A0A6L0ZRP4_YEASX 1-252  
uS3 | BJ4_G0045400.mRNA.1.CDS.1 | A0A6L0ZVK6_YEASX 1-240  
uS4 | BJ4_G0026100.mRNA.1.CDS.1 | A0A7I9GPQ3_YEASX 1-197  
uS5 | 40S ribosomal protein S2 | A0A6A5PWF7_YEASX 1-254  
uS7 | Rps5p | A0A1L4AA68_YEASX 1-225  
uS8 | 40S ribosomal protein S22-A | A0A6A5PSE9_YEASX 1-130  
uS9 | BJ4_G0008010.mRNA.1.CDS.1 | A0A6L0YQ58_YEASX 1-143  
  
Non-standard residues in 7osm #4  
---  
DDE — {3-[4-(2-amino-2-carboxy-ethyl)-1H-imidazol-2-yl]-1-carbamoyl-
propyl}-trimethyl-ammonium (diphthamide;
2-(3-carboxyamido-3-(trimethylammonio)propyl)histidine)  
GTP — guanosine-5'-triphosphate  
MG — magnesium ion  
YG — wybutosine (Y-base; 1H-imidazo(1,2-α)purine-7-butanoic
acid,4,9-dihydro-α-((methoxycarbonyl)amino)-4,6-dimethyl-9-oxo-methyl ester)  
ZN — zinc ion  
  
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open
> /Volumes/sd18G003/SubtomoAveraging/Chimera_Templates_ForID/Yeast_RibosomalStates/EMD-12059_PRE1.mrc

Opened EMD-12059_PRE1.mrc as #5, grid size 420,420,420, pixel 1.08, shown at
level 0.0451, step 2, values float32  

> open
> /Volumes/sd18G003/SubtomoAveraging/Chimera_Templates_ForID/Yeast_RibosomalStates/EMD*

Opened EMD-12059_PRE1.mrc as #6.1, grid size 420,420,420, pixel 1.08, shown at
level 0.0451, step 2, values float32  
Opened EMD-12061_PRE2.mrc as #6.2, grid size 420,420,420, pixel 1.08, shown at
level 0.0416, step 2, values float32  
Opened EMD-12062_POST2.mrc as #6.3, grid size 420,420,420, pixel 1.08, shown
at level 0.0447, step 2, values float32  
Opened EMD-12064_POST3.mrc as #6.4, grid size 420,420,420, pixel 1.08, shown
at level 0.0444, step 2, values float32  
Opened EMD-12065_PRE4.mrc as #6.5, grid size 420,420,420, pixel 1.08, shown at
level 0.0481, step 2, values float32  
Opened EMD-12074_POST1.mrc as #6.6, grid size 420,420,420, pixel 1.08, shown
at level 0.038, step 2, values float32  
Opened EMD-12075_PRE3.mrc as #6.7, grid size 420,420,420, pixel 1.08, shown at
level 0.04, step 2, values float32  

> close #5

> rename #6.1 id #51

> rename #6.2 id #52

> rename #6.7 id #53

> rename #6.5 id #54

> rename #6.6 id #55

> rename #6.3 id #56

> rename #6.4 id #57

> close #6

> rename #1 id #50

> rename #2 id #58

> rename #3 id #59

> rename #4 id #60

> hide #!57 models

> hide #!56 models

> hide #!55 models

> hide #!54 models

> hide #!53 models

> hide #!52 models

> hide #!51 models

> hide #!60 models

> select add #58

209136 atoms, 224719 bonds, 4513 pseudobonds, 17082 residues, 3 models
selected  

> select add #59

416887 atoms, 447826 bonds, 8941 pseudobonds, 34146 residues, 6 models
selected  

> ui mousemode right "translate selected models"

> view matrix models
> #58,1,0,0,-117.54,0,1,0,292.39,0,0,1,120.16,#59,1,0,0,-117.54,0,1,0,292.39,0,0,1,120.16

> view matrix models
> #58,0.047802,-0.56438,0.82413,-9.4466,0.18248,0.81612,0.54831,190.81,-0.98205,0.12418,0.142,427.21,#59,0.047802,-0.56438,0.82413,-9.4466,0.18248,0.81612,0.54831,190.81,-0.98205,0.12418,0.142,427.21

> view matrix models
> #58,-0.93505,0.1888,-0.30007,243.43,0.21314,-0.377,-0.90136,644.4,-0.2833,-0.90677,0.31227,442.92,#59,-0.93505,0.1888,-0.30007,243.43,0.21314,-0.377,-0.90136,644.4,-0.2833,-0.90677,0.31227,442.92

> view matrix models
> #58,-0.93505,0.1888,-0.30007,441.53,0.21314,-0.377,-0.90136,465.28,-0.2833,-0.90677,0.31227,431.52,#59,-0.93505,0.1888,-0.30007,441.53,0.21314,-0.377,-0.90136,465.28,-0.2833,-0.90677,0.31227,431.52

> view matrix models
> #58,-0.98435,0.16015,-0.073522,413.56,0.039404,-0.20661,-0.97763,481.6,-0.17176,-0.96523,0.19707,442.61,#59,-0.98435,0.16015,-0.073522,413.56,0.039404,-0.20661,-0.97763,481.6,-0.17176,-0.96523,0.19707,442.61

> view matrix models
> #58,-0.98435,0.16015,-0.073522,406.83,0.039404,-0.20661,-0.97763,478.19,-0.17176,-0.96523,0.19707,430.64,#59,-0.98435,0.16015,-0.073522,406.83,0.039404,-0.20661,-0.97763,478.19,-0.17176,-0.96523,0.19707,430.64

> view matrix models
> #58,-0.99467,-0.059558,-0.084223,446.48,0.089527,-0.092834,-0.99165,453.41,0.051242,-0.9939,0.097671,414.56,#59,-0.99467,-0.059558,-0.084223,446.48,0.089527,-0.092834,-0.99165,453.41,0.051242,-0.9939,0.097671,414.56

> view matrix models
> #58,-0.99467,-0.059558,-0.084223,461.63,0.089527,-0.092834,-0.99165,447.36,0.051242,-0.9939,0.097671,407.26,#59,-0.99467,-0.059558,-0.084223,461.63,0.089527,-0.092834,-0.99165,447.36,0.051242,-0.9939,0.097671,407.26

> hide #!58 models

> hide #!59 models

> select subtract #58

207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models
selected  

> select subtract #59

Nothing selected  

> select add #60

207066 atoms, 221714 bonds, 5069 pseudobonds, 17603 residues, 4 models
selected  

> show #!60 models

> view matrix models #60,1,0,0,30.223,0,1,0,-76.385,0,0,1,86.982

> view matrix models
> #60,-0.1909,-0.6662,0.72092,-79.235,0.2144,-0.745,-0.63168,-29.647,0.95791,0.033981,0.28505,182.3

> view matrix models
> #60,-0.1909,-0.6662,0.72092,272.21,0.2144,-0.745,-0.63168,99.433,0.95791,0.033981,0.28505,145.82

> view matrix models
> #60,-0.1909,-0.6662,0.72092,231.98,0.2144,-0.745,-0.63168,288.75,0.95791,0.033981,0.28505,256.4

> view matrix models
> #60,-0.1909,-0.6662,0.72092,220.48,0.2144,-0.745,-0.63168,271.39,0.95791,0.033981,0.28505,273.19

> view matrix models
> #60,-0.1909,-0.6662,0.72092,200.51,0.2144,-0.745,-0.63168,287.71,0.95791,0.033981,0.28505,279.52

> view matrix models
> #60,-0.1943,-0.64929,0.7353,199.48,0.18966,-0.76031,-0.62126,285.72,0.96243,0.018745,0.27087,280.61

> view matrix models
> #60,-0.19366,-0.64908,0.73565,199.49,0.18995,-0.76047,-0.62097,285.71,0.9625,0.019475,0.27057,280.64

> view matrix models
> #60,-0.19366,-0.64908,0.73565,58.411,0.18995,-0.76047,-0.62097,290.37,0.9625,0.019475,0.27057,425.03

> view matrix models
> #60,-0.19366,-0.64908,0.73565,68.216,0.18995,-0.76047,-0.62097,298.2,0.9625,0.019475,0.27057,398.35

> view matrix models
> #60,-0.15452,-0.63129,0.76,68.815,0.16318,-0.77498,-0.61056,296.1,0.97442,0.029671,0.22276,401.98

> view matrix models
> #60,-0.063398,-0.58719,0.80696,70.821,0.37414,-0.7636,-0.52625,302.06,0.9252,0.26855,0.2681,397.09

> view matrix models
> #60,-0.063398,-0.58719,0.80696,200.63,0.37414,-0.7636,-0.52625,291.05,0.9252,0.26855,0.2681,277.96

> view matrix models
> #60,-0.077351,-0.71118,0.69874,206.35,0.27899,-0.68829,-0.66965,295.1,0.95717,0.14314,0.25165,280.39

> view matrix models
> #60,-0.077351,-0.71118,0.69874,172.53,0.27899,-0.68829,-0.66965,285.5,0.95717,0.14314,0.25165,259.59

> view matrix models
> #60,-0.11357,-0.63814,0.7615,166.87,0.16776,-0.76777,-0.61837,276.24,0.97926,0.05752,0.19425,264.14

> view matrix models
> #60,-0.065429,-0.38484,0.92066,160.09,0.3426,-0.87522,-0.3415,268.04,0.9372,0.29308,0.18911,262.76

> view matrix models
> #60,-0.089808,-0.55289,0.8284,164.16,0.23079,-0.82068,-0.52271,273.51,0.96885,0.14425,0.20131,263.34

> view matrix models
> #60,-0.40852,-0.31261,0.85755,146,0.017455,-0.94202,-0.33509,250.26,0.91258,-0.12192,0.39029,248.01

> view matrix models
> #60,-0.40852,-0.31261,0.85755,187.02,0.017455,-0.94202,-0.33509,265.7,0.91258,-0.12192,0.39029,271.54

> fitmap #60 inMap #50

Fit molecule 7osm (#60) to map Stable_60S.mrc (#50) using 207066 atoms  
average map value = 0.5435, steps = 140  
shifted from previous position = 19.7  
rotated from previous position = 20.6 degrees  
atoms outside contour = 120599, contour level = 0.78541  
  
Position of 7osm (#60) relative to Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
-0.63997038 -0.43579527 0.63286681 170.45881580  
0.18921705 -0.88763255 -0.41988733 275.56308451  
0.74473809 -0.14896626 0.65051843 258.43697340  
Axis 0.39245224 -0.16205507 0.90538356  
Axis point -1.96148654 167.78399005 0.00000000  
Rotation angle (degrees) 159.80816941  
Shift along axis 256.22513556  
  

> select subtract #60

Nothing selected  

> hide #!60 models

> show #!59 models

> show #!58 models

> fitmap #58,59 inMap #50 eachModel true

Fit molecule 3j78 (#58) to map Stable_60S.mrc (#50) using 209136 atoms  
average map value = 0.536, steps = 120  
shifted from previous position = 14.2  
rotated from previous position = 7.72 degrees  
atoms outside contour = 124816, contour level = 0.78541  
  
Position of 3j78 (#58) relative to Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
-0.98102588 0.01790903 -0.19304790 463.65700684  
0.19035572 -0.09993326 -0.97661561 413.13011549  
-0.03678215 -0.99483296 0.09462803 421.25284843  
Axis -0.07804262 -0.66943825 0.73875692  
Axis point 237.74694936 415.79906020 -0.00000000  
Rotation angle (degrees) 173.29749896  
Shift along axis -1.54665500  
  
Fit molecule 3j77 (#59) to map Stable_60S.mrc (#50) using 207751 atoms  
average map value = 0.5386, steps = 104  
shifted from previous position = 13.9  
rotated from previous position = 7.09 degrees  
atoms outside contour = 123766, contour level = 0.78541  
  
Position of 3j77 (#59) relative to Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
-0.98556694 0.03244676 -0.16614759 456.60442131  
0.16277054 -0.08804099 -0.98272811 417.68563668  
-0.04651414 -0.99558826 0.08148891 425.91785735  
Axis -0.07250270 -0.67446685 0.73473657  
Axis point 236.72585691 418.13478086 0.00000000  
Rotation angle (degrees) 174.91190029  
Shift along axis -1.88274629  
  

> hide #!58 models

> hide #!59 models

> show #!51 models

> show #!52 models

> show #53-57

> hide #!50 models

> show #!50 models

> hide #!52 models

> hide #!53 models

> hide #!54 models

> hide #!55 models

> hide #!56 models

> hide #!57 models

> select add #51

2 models selected  

> view matrix models #51,1,0,0,-267.42,0,1,0,-49.624,0,0,1,51.868

> view matrix models
> #51,0.41873,-0.62266,0.66103,-144.85,0.47864,0.76993,0.42203,-186.92,-0.77173,0.13968,0.62042,261.92

> view matrix models
> #51,0.389,-0.63409,0.66828,-137.58,0.48271,0.75816,0.43839,-188.57,-0.78464,0.15206,0.60101,265.92

> view matrix models
> #51,-0.64044,0.45125,0.62146,-123,-0.13992,0.72709,-0.67213,162.27,-0.75515,-0.51742,-0.40252,583.08

> view matrix models
> #51,-0.86338,0.21384,-0.45699,176.89,0.48883,0.13022,-0.8626,181.91,-0.12495,-0.96815,-0.21697,501.97

> view matrix models
> #51,-0.93545,0.084084,-0.34332,196.48,0.3491,0.06759,-0.93464,238,-0.055383,-0.99416,-0.092581,468.55

> view matrix models
> #51,-0.93545,0.084084,-0.34332,499.97,0.3491,0.06759,-0.93464,367.05,-0.055383,-0.99416,-0.092581,543.36

> view matrix models
> #51,-0.9416,0.14666,-0.30313,481.24,0.31197,0.040993,-0.94921,383.06,-0.12678,-0.98834,-0.084352,555.96

> view matrix models
> #51,-0.98147,0.045878,-0.18602,487.52,0.18529,-0.019884,-0.98248,428.64,-0.048773,-0.99875,0.011015,523.16

> view matrix models
> #51,-0.9873,0.11812,-0.10625,459.29,0.11491,0.069092,-0.99097,427.71,-0.10971,-0.99059,-0.081787,552.25

> view matrix models
> #51,-0.9873,0.11812,-0.10625,455.45,0.11491,0.069092,-0.99097,439.58,-0.10971,-0.99059,-0.081787,540.5

> view matrix models
> #51,-0.9873,0.11812,-0.10625,471.82,0.11491,0.069092,-0.99097,414.48,-0.10971,-0.99059,-0.081787,506.76

> view matrix models
> #51,-0.9889,0.093681,-0.11532,478.74,0.11984,0.044083,-0.99181,418.54,-0.08783,-0.99463,-0.054821,497.73

> view matrix models
> #51,-0.98704,0.11837,-0.10838,472.12,0.11134,0.018649,-0.99361,425.75,-0.1156,-0.99279,-0.031587,498.91

> view matrix models
> #51,-0.98785,0.12141,-0.096995,466.7,0.10081,0.025683,-0.99457,430.49,-0.11826,-0.99227,-0.037611,503.62

> view matrix models
> #51,-0.96766,0.078848,-0.23962,497.92,0.23822,-0.026935,-0.97084,406.93,-0.083003,-0.99652,0.0072808,488.37

> view matrix models
> #51,-0.96766,0.078848,-0.23962,495.76,0.23822,-0.026935,-0.97084,409.67,-0.083003,-0.99652,0.0072808,491.65

> view matrix models
> #51,-0.96766,0.078848,-0.23962,494.37,0.23822,-0.026935,-0.97084,408.77,-0.083003,-0.99652,0.0072808,489.92

> fitmap #51-57 inMap #50 eachModel false

Multiple maps for #51-57  

> fitmap #51-57 inMap #50

Multiple maps for #51-57  

> fitmap #51-57 inMap #50

Multiple maps for #51-57  

> fitmap #51-57 inMap #50 eachModel true

Fit map EMD-12059_PRE1.mrc in map Stable_60S.mrc using 92586 points  
correlation = 0.7934, correlation about mean = 0.2582, overlap = 4659  
steps = 100, shift = 9.53, angle = 6.76 degrees  
  
Position of EMD-12059_PRE1.mrc (#51) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
-0.98788767 0.05118552 -0.14648547 490.76807290  
0.14187690 -0.08435513 -0.98628351 453.98836765  
-0.06284023 -0.99512022 0.07607135 472.88600604  
Axis -0.07144167 -0.67624183 0.73320739  
Axis point 258.77332438 455.43300803 0.00000000  
Rotation angle (degrees) 176.45424201  
Shift along axis 4.65630110  
  
Fit map EMD-12061_PRE2.mrc in map Stable_60S.mrc using 92518 points  
correlation = 0.7775, correlation about mean = 0.1955, overlap = 3041  
steps = 188, shift = 27.7, angle = 37.8 degrees  
  
Position of EMD-12061_PRE2.mrc (#52) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.79011675 -0.60167214 -0.11707329 201.19363740  
0.59899339 0.79843877 -0.06084775 -57.34886433  
0.13008625 -0.02204930 0.99125748 -33.34908009  
Axis 0.03163464 -0.20152359 0.97897267  
Axis point 191.05318731 268.51937514 0.00000000  
Rotation angle (degrees) 37.82322508  
Shift along axis -14.72600065  
  
Fit map EMD-12075_PRE3.mrc in map Stable_60S.mrc using 92602 points  
correlation = 0.7786, correlation about mean = 0.1706, overlap = 2906  
steps = 156, shift = 28.2, angle = 36.5 degrees  
  
Position of EMD-12075_PRE3.mrc (#53) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.80499358 -0.58571279 -0.09447675 189.86481995  
0.58158900 0.81051817 -0.06938689 -53.20671130  
0.11721591 0.00090937 0.99310604 -38.26918018  
Axis 0.05915088 -0.17812907 0.98222768  
Axis point 182.97467338 264.94571251 0.00000000  
Rotation angle (degrees) 36.45643600  
Shift along axis -16.88071446  
  
Fit map EMD-12065_PRE4.mrc in map Stable_60S.mrc using 92599 points  
correlation = 0.7668, correlation about mean = 0.224, overlap = 4192  
steps = 192, shift = 29.5, angle = 39.2 degrees  
  
Position of EMD-12065_PRE4.mrc (#54) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.77722807 -0.62453842 -0.07660480 199.93471210  
0.61720065 0.78039292 -0.10025092 -45.98020557  
0.12239239 0.03063729 0.99200880 -47.17160835  
Axis 0.10351998 -0.15738763 0.98209610  
Axis point 172.31047256 261.71781049 0.00000000  
Rotation angle (degrees) 39.21174668  
Shift along axis -18.39310044  
  
Fit map EMD-12074_POST1.mrc in map Stable_60S.mrc using 92601 points  
correlation = 0.7779, correlation about mean = 0.1978, overlap = 2745  
steps = 176, shift = 27.1, angle = 35.3 degrees  
  
Position of EMD-12074_POST1.mrc (#55) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.81587898 -0.56669392 -0.11488906 185.75318274  
0.56641476 0.82323211 -0.03825197 -63.21526421  
0.11625753 -0.03386588 0.99264157 -26.51809116  
Axis 0.00379271 -0.19987549 0.97981396  
Axis point 198.28401075 263.44535221 0.00000000  
Rotation angle (degrees) 35.32589643  
Shift along axis -12.64310605  
  
Fit map EMD-12062_POST2.mrc in map Stable_60S.mrc using 92597 points  
correlation = 0.7677, correlation about mean = 0.198, overlap = 3286  
steps = 196, shift = 28.4, angle = 38.5 degrees  
  
Position of EMD-12062_POST2.mrc (#56) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.78496248 -0.61729953 -0.05268005 193.14619740  
0.61228963 0.78593601 -0.08605812 -49.96253957  
0.09452678 0.03529694 0.99489638 -41.48085466  
Axis 0.09752866 -0.11830479 0.98817617  
Axis point 173.85171614 254.89350983 0.00000000  
Rotation angle (degrees) 38.47336712  
Shift along axis -16.24229530  
  
Fit map EMD-12064_POST3.mrc in map Stable_60S.mrc using 92531 points  
correlation = 0.7682, correlation about mean = 0.1834, overlap = 3249  
steps = 176, shift = 29.2, angle = 36.9 degrees  
  
Position of EMD-12064_POST3.mrc (#57) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.80094894 -0.59277382 -0.08426152 189.38572704  
0.58630774 0.80504344 -0.09026790 -47.24274355  
0.12134263 0.02289680 0.99234656 -44.30861819  
Axis 0.09413044 -0.17102160 0.98076046  
Axis point 173.48703920 264.02128291 0.00000000  
Rotation angle (degrees) 36.94913442  
Shift along axis -17.54964951  
  

> show #!52 models

> show #!53 models

> hide #!51 models

> undo

[Repeated 9 time(s)]

> show #!52 models

> undo

> show #!52 models

> hide #!52 models

> view orient

> show #!52 models

> select add #52

4 models selected  

> view orient

> view matrix models
> #51,-0.9873,0.11812,-0.10625,665.68,0.11491,0.069092,-0.99097,437.86,-0.10971,-0.99059,-0.081787,713.53,#52,0.79012,-0.60167,-0.11707,411.42,0.59899,0.79844,-0.060848,-59.071,0.13009,-0.022049,0.99126,139.68

> show #!53 models

> view matrix models
> #51,-0.9873,0.11812,-0.10625,453.13,0.11491,0.069092,-0.99097,436.84,-0.10971,-0.99059,-0.081787,537.83,#52,0.79012,-0.60167,-0.11707,198.87,0.59899,0.79844,-0.060848,-60.088,0.13009,-0.022049,0.99126,-36.024

> hide #!53 models

> select subtract #52

2 models selected  

> view matrix models
> #51,-0.9873,0.11812,-0.10625,624.76,0.11491,0.069092,-0.99097,446.27,-0.10971,-0.99059,-0.081787,682.08

> view matrix models
> #51,-0.82399,0.10371,-0.55702,678.25,0.54785,0.39662,-0.73658,240.07,0.14453,-0.91211,-0.38363,669.33

> view matrix models
> #51,-0.99427,0.094718,-0.049503,620.11,0.10558,0.79867,-0.59243,227.85,-0.016577,-0.59427,-0.8041,720.79

> view matrix models
> #51,-0.7825,0.49712,-0.37491,556.72,0.55502,0.82981,-0.058113,23.682,0.28222,-0.25356,-0.92524,612.13

> view matrix models
> #51,0.51579,-0.79289,-0.32447,524.35,0.70818,0.60774,-0.35936,92.107,0.48213,-0.044432,0.87497,185.61

> view matrix models
> #51,0.6317,-0.69321,-0.347,483.99,0.55935,0.71751,-0.4151,112.87,0.53673,0.068125,0.841,158.03

> view matrix models
> #51,0.6317,-0.69321,-0.347,265.71,0.55935,0.71751,-0.4151,18.041,0.53673,0.068125,0.841,-48.285

> view matrix models
> #51,0.6317,-0.69321,-0.347,327.33,0.55935,0.71751,-0.4151,54.388,0.53673,0.068125,0.841,-110.28

> view matrix models
> #51,0.6317,-0.69321,-0.347,325.15,0.55935,0.71751,-0.4151,46.772,0.53673,0.068125,0.841,-114.94

> view matrix models
> #51,0.70792,-0.70616,-0.013894,248.05,0.64331,0.65278,-0.40003,38.726,0.29156,0.27425,0.9164,-117.54

> view matrix models
> #51,0.70792,-0.70616,-0.013894,185.6,0.64331,0.65278,-0.40003,44.312,0.29156,0.27425,0.9164,-107.57

> view matrix models
> #51,0.70792,-0.70616,-0.013894,204.82,0.64331,0.65278,-0.40003,32.248,0.29156,0.27425,0.9164,-91.365

> view matrix models
> #51,0.73543,-0.67752,-0.010913,192.67,0.62793,0.68748,-0.3648,21.972,0.25466,0.26143,0.93102,-83.685

> view matrix models
> #51,0.66586,-0.74522,-0.035708,225.73,0.71223,0.64919,-0.26699,-7.1153,0.22214,0.15234,0.96304,-61.161

> view matrix models
> #51,0.62981,-0.77367,0.069075,219.19,0.75701,0.59147,-0.27767,-3.2487,0.17397,0.22717,0.95819,-64.74

> view matrix models
> #51,0.62981,-0.77367,0.069075,239.81,0.75701,0.59147,-0.27767,1.2566,0.17397,0.22717,0.95819,-91.851

> fitmap #51 inMap #52 eachModel true

Fit map EMD-12059_PRE1.mrc in map EMD-12061_PRE2.mrc using 92586 points  
correlation = 0.9066, correlation about mean = 0.5481, overlap = 379.5  
steps = 348, shift = 6.91, angle = 21.5 degrees  
  
Position of EMD-12059_PRE1.mrc (#51) relative to EMD-12061_PRE2.mrc (#52)
coordinates:  
Matrix rotation and translation  
0.99975230 0.00771994 0.02087468 -5.93953199  
-0.00772256 0.99997019 0.00004472 1.29341661  
-0.02087371 -0.00020591 0.99978210 5.35355907  
Axis -0.00563052 0.93787915 -0.34691640  
Axis point 243.32154542 0.00000000 287.58494812  
Rotation angle (degrees) 1.27532626  
Shift along axis -0.61072630  
  

> hide #!52 models

> select add #52

4 models selected  

> select add #53

6 models selected  

> select add #54

8 models selected  

> select add #55

10 models selected  

> select add #56

12 models selected  

> select add #57

14 models selected  

> view matrix models
> #51,0.79701,-0.59553,-0.10058,290.95,0.59395,0.80305,-0.048295,-232.67,0.10953,-0.021248,0.99376,211.15,#52,0.79012,-0.60167,-0.11707,297.05,0.59899,0.79844,-0.060848,-229.82,0.13009,-0.022049,0.99126,206.64,#53,0.80499,-0.58571,-0.094477,288.04,0.58159,0.81052,-0.069387,-222.94,0.11722,0.00090937,0.99311,204.4,#54,0.77723,-0.62454,-0.076605,298.11,0.6172,0.78039,-0.10025,-215.72,0.12239,0.030637,0.99201,195.49,#55,0.81588,-0.56669,-0.11489,283.93,0.56641,0.82323,-0.038252,-232.95,0.11626,-0.033866,0.99264,216.15,#56,0.78496,-0.6173,-0.05268,291.32,0.61229,0.78594,-0.086058,-219.7,0.094527,0.035297,0.9949,201.19,#57,0.80095,-0.59277,-0.084262,287.56,0.58631,0.80504,-0.090268,-216.98,0.12134,0.022897,0.99235,198.36

> show #!54 models

> hide #!54 models

> view matrix models
> #51,0.79701,-0.59553,-0.10058,189.26,0.59395,0.80305,-0.048295,-219.14,0.10953,-0.021248,0.99376,120.12,#52,0.79012,-0.60167,-0.11707,195.36,0.59899,0.79844,-0.060848,-216.29,0.13009,-0.022049,0.99126,115.62,#53,0.80499,-0.58571,-0.094477,186.36,0.58159,0.81052,-0.069387,-209.4,0.11722,0.00090937,0.99311,113.37,#54,0.77723,-0.62454,-0.076605,196.43,0.6172,0.78039,-0.10025,-202.18,0.12239,0.030637,0.99201,104.47,#55,0.81588,-0.56669,-0.11489,182.24,0.56641,0.82323,-0.038252,-219.41,0.11626,-0.033866,0.99264,125.12,#56,0.78496,-0.6173,-0.05268,189.64,0.61229,0.78594,-0.086058,-206.16,0.094527,0.035297,0.9949,110.16,#57,0.80095,-0.59277,-0.084262,185.88,0.58631,0.80504,-0.090268,-203.44,0.12134,0.022897,0.99235,107.33

> view matrix models
> #51,0.68984,0.70829,-0.14982,-36.931,0.42791,-0.56583,-0.70479,212.72,-0.58397,0.42208,-0.69342,501.7,#52,0.69201,0.70294,-0.16433,-32.85,0.40873,-0.56915,-0.71345,219.7,-0.59504,0.42655,-0.68117,501.26,#53,0.67812,0.7151,-0.16968,-27.156,0.43102,-0.57394,-0.69629,213.25,-0.5953,0.39903,-0.69741,508.97,#54,0.70879,0.67722,-0.19745,-17.805,0.40098,-0.61708,-0.67707,225.31,-0.58037,0.40073,-0.70893,509.42,#55,0.6648,0.73343,-0.14186,-38.649,0.4423,-0.5395,-0.71646,204.3,-0.602,0.41355,-0.68306,502.42,#56,0.70752,0.68331,-0.18029,-23.205,0.42547,-0.61557,-0.66337,217.23,-0.56427,0.39264,-0.72625,509.38,#57,0.68182,0.70675,-0.18873,-20.812,0.42455,-0.59242,-0.68468,215.78,-0.59571,0.38671,-0.70398,514.04

> view matrix models
> #51,-0.83705,0.2801,0.47,257.82,-0.44785,0.1427,-0.88265,293.95,-0.3143,-0.94931,0.0059995,582.84,#52,-0.82487,0.28658,0.48731,249.94,-0.46506,0.14611,-0.87314,295.67,-0.32142,-0.94685,0.012754,582.09,#53,-0.8376,0.27743,0.4706,255.02,-0.45647,0.11783,-0.8819,300.19,-0.30012,-0.95349,0.027946,572.75,#54,-0.82172,0.33151,0.46355,240.73,-0.45534,0.10719,-0.88384,304.12,-0.34269,-0.93734,0.062871,569.12,#55,-0.84307,0.24407,0.47923,265.94,-0.45777,0.14204,-0.87765,291.81,-0.28228,-0.9593,-0.0080212,580.86,#56,-0.83738,0.32522,0.43935,249.99,-0.43165,0.099702,-0.89652,301.66,-0.33537,-0.94037,0.056891,570.72,#57,-0.8339,0.29339,0.46747,251.45,-0.45939,0.10049,-0.88253,305.32,-0.3059,-0.9507,0.050985,566.98

> view matrix models
> #51,-0.97793,-0.19105,0.084585,454.74,-0.077138,-0.046099,-0.99595,273.37,0.19417,-0.9805,0.030344,475.29,#52,-0.9774,-0.18349,0.10502,448.61,-0.098265,-0.045546,-0.99412,278.17,0.18719,-0.98197,0.026486,477.53,#53,-0.97433,-0.2036,0.096055,449.64,-0.083842,-0.067804,-0.99417,279.57,0.20893,-0.9767,0.048994,466.11,#54,-0.982,-0.15575,0.10682,437.68,-0.092078,-0.098971,-0.99082,288.86,0.16489,-0.98283,0.082849,468.01,#55,-0.97045,-0.22515,0.086836,459.58,-0.081639,-0.03231,-0.99614,267.93,0.22708,-0.97379,0.012974,470.67,#56,-0.98306,-0.16481,0.080153,445.09,-0.063608,-0.10333,-0.99261,282.88,0.17187,-0.9809,0.091098,466.11,#57,-0.97517,-0.19521,0.1046,445.67,-0.088389,-0.090007,-0.99201,285.36,0.20307,-0.97662,0.070517,461.3

> view matrix models
> #51,-0.98951,-0.13677,0.046522,453.69,-0.044931,-0.014697,-0.99888,260.79,0.1373,-0.99049,0.0083975,493.65,#52,-0.98935,-0.12912,0.067194,447.62,-0.065885,-0.014394,-0.99772,265.76,0.1298,-0.99152,0.0057337,495.67,#53,-0.987,-0.1503,0.056975,449.35,-0.052127,-0.036,-0.99799,267.4,0.15205,-0.98799,0.027698,484.37,#54,-0.99246,-0.10334,0.065916,437.65,-0.05898,-0.068791,-0.99589,277.09,0.10745,-0.99226,0.062177,485.84,#55,-0.98407,-0.17067,0.049745,458.58,-0.05052,0.00019957,-0.99872,255.28,0.17044,-0.98533,-0.0088188,489.17,#56,-0.99288,-0.11265,0.038781,444.93,-0.030671,-0.072852,-0.99687,270.88,0.11512,-0.99096,0.068878,484.2,#57,-0.98767,-0.14274,0.06436,445.88,-0.056493,-0.058499,-0.99669,273.45,0.14603,-0.98803,0.049714,479.5

> view matrix models
> #51,-0.97091,-0.2123,-0.11078,494.57,0.13165,-0.086774,-0.98749,235.03,0.20003,-0.97334,0.1122,457.06,#52,-0.97462,-0.2048,-0.090447,489.54,0.11033,-0.087832,-0.99001,241.09,0.19481,-0.97486,0.1082,458.9,#53,-0.96844,-0.22878,-0.098881,490.63,0.12558,-0.10523,-0.98649,241.34,0.21528,-0.96777,0.13063,447.4,#54,-0.97829,-0.18803,-0.087125,480.75,0.11548,-0.14554,-0.98259,252.92,0.17207,-0.97132,0.1641,448.53,#55,-0.96391,-0.24294,-0.10889,498.18,0.12844,-0.066083,-0.98951,228.39,0.2332,-0.96779,0.094901,452.9,#56,-0.97366,-0.19773,-0.11349,486.82,0.14408,-0.14788,-0.97846,245.46,0.17669,-0.96904,0.17247,447.12,#57,-0.97024,-0.22488,-0.08973,487.8,0.12083,-0.12856,-0.98431,247.38,0.20982,-0.96587,0.15191,442.13

> view matrix models
> #51,-0.97393,-0.1819,-0.13551,493.9,0.14991,-0.067849,-0.98637,227.14,0.17023,-0.98097,0.09335,468.55,#52,-0.97793,-0.17438,-0.11512,488.93,0.12876,-0.069049,-0.98927,233.29,0.16456,-0.98225,0.089978,470.31,#53,-0.97211,-0.19895,-0.12421,490.41,0.14357,-0.086015,-0.98589,233.68,0.18546,-0.97623,0.11218,458.86,#54,-0.98074,-0.15897,-0.11348,480.75,0.13432,-0.12716,-0.98274,245.45,0.1418,-0.97906,0.14606,459.85,#55,-0.96811,-0.21226,-0.1331,497.5,0.14607,-0.046576,-0.98818,220.49,0.20355,-0.9761,0.076095,464.41,#56,-0.97566,-0.1688,-0.14001,486.7,0.16274,-0.12931,-0.97816,237.89,0.14701,-0.97713,0.15363,458.53,#57,-0.97383,-0.19562,-0.11572,487.88,0.13894,-0.10945,-0.98423,239.86,0.17987,-0.97455,0.13377,453.6

> view matrix models
> #51,-0.97393,-0.1819,-0.13551,632.17,0.14991,-0.067849,-0.98637,358.05,0.17023,-0.98097,0.09335,365.86,#52,-0.97793,-0.17438,-0.11512,627.2,0.12876,-0.069049,-0.98927,364.2,0.16456,-0.98225,0.089978,367.63,#53,-0.97211,-0.19895,-0.12421,628.68,0.14357,-0.086015,-0.98589,364.59,0.18546,-0.97623,0.11218,356.18,#54,-0.98074,-0.15897,-0.11348,619.02,0.13432,-0.12716,-0.98274,376.37,0.1418,-0.97906,0.14606,357.16,#55,-0.96811,-0.21226,-0.1331,635.77,0.14607,-0.046576,-0.98818,351.4,0.20355,-0.9761,0.076095,361.73,#56,-0.97566,-0.1688,-0.14001,624.97,0.16274,-0.12931,-0.97816,368.8,0.14701,-0.97713,0.15363,355.84,#57,-0.97383,-0.19562,-0.11572,626.15,0.13894,-0.10945,-0.98423,370.77,0.17987,-0.97455,0.13377,350.92

> view matrix models
> #51,-0.97393,-0.1819,-0.13551,572.63,0.14991,-0.067849,-0.98637,460.15,0.17023,-0.98097,0.09335,398.29,#52,-0.97793,-0.17438,-0.11512,567.66,0.12876,-0.069049,-0.98927,466.3,0.16456,-0.98225,0.089978,400.06,#53,-0.97211,-0.19895,-0.12421,569.15,0.14357,-0.086015,-0.98589,466.69,0.18546,-0.97623,0.11218,388.61,#54,-0.98074,-0.15897,-0.11348,559.48,0.13432,-0.12716,-0.98274,478.46,0.1418,-0.97906,0.14606,389.59,#55,-0.96811,-0.21226,-0.1331,576.23,0.14607,-0.046576,-0.98818,453.5,0.20355,-0.9761,0.076095,394.16,#56,-0.97566,-0.1688,-0.14001,565.43,0.16274,-0.12931,-0.97816,470.9,0.14701,-0.97713,0.15363,388.27,#57,-0.97383,-0.19562,-0.11572,566.61,0.13894,-0.10945,-0.98423,472.87,0.17987,-0.97455,0.13377,383.35

> view matrix models
> #51,-0.97393,-0.1819,-0.13551,564.96,0.14991,-0.067849,-0.98637,462.97,0.17023,-0.98097,0.09335,404.17,#52,-0.97793,-0.17438,-0.11512,559.99,0.12876,-0.069049,-0.98927,469.12,0.16456,-0.98225,0.089978,405.93,#53,-0.97211,-0.19895,-0.12421,561.47,0.14357,-0.086015,-0.98589,469.51,0.18546,-0.97623,0.11218,394.48,#54,-0.98074,-0.15897,-0.11348,551.81,0.13432,-0.12716,-0.98274,481.28,0.1418,-0.97906,0.14606,395.47,#55,-0.96811,-0.21226,-0.1331,568.56,0.14607,-0.046576,-0.98818,456.32,0.20355,-0.9761,0.076095,400.03,#56,-0.97566,-0.1688,-0.14001,557.76,0.16274,-0.12931,-0.97816,473.72,0.14701,-0.97713,0.15363,394.15,#57,-0.97383,-0.19562,-0.11572,558.94,0.13894,-0.10945,-0.98423,475.69,0.17987,-0.97455,0.13377,389.22

> view matrix models
> #51,-0.95604,-0.23125,-0.18031,579.42,0.20307,-0.07852,-0.97601,451.71,0.21154,-0.96972,0.12203,387.62,#52,-0.96135,-0.22387,-0.16026,574.85,0.18204,-0.080129,-0.98002,458.14,0.20655,-0.97132,0.11778,389.47,#53,-0.95382,-0.24894,-0.16812,575.81,0.19695,-0.095688,-0.97573,458.22,0.22681,-0.96378,0.1403,377.96,#54,-0.96496,-0.21126,-0.15565,566.81,0.18727,-0.13888,-0.97244,470.49,0.18383,-0.96751,0.17357,379.12,#55,-0.94884,-0.26024,-0.1788,582.48,0.19961,-0.055625,-0.9783,444.8,0.24464,-0.96394,0.10473,383.48,#56,-0.95821,-0.22108,-0.18153,572.3,0.21549,-0.14048,-0.96635,462.61,0.18814,-0.96508,0.18225,377.7,#57,-0.95603,-0.24672,-0.15854,573.35,0.1923,-0.11923,-0.97407,464.42,0.22142,-0.96172,0.16143,372.68

> view matrix models
> #51,-0.95604,-0.23125,-0.18031,561.64,0.20307,-0.07852,-0.97601,440.77,0.21154,-0.96972,0.12203,385.13,#52,-0.96135,-0.22387,-0.16026,557.07,0.18204,-0.080129,-0.98002,447.2,0.20655,-0.97132,0.11778,386.99,#53,-0.95382,-0.24894,-0.16812,558.03,0.19695,-0.095688,-0.97573,447.28,0.22681,-0.96378,0.1403,375.47,#54,-0.96496,-0.21126,-0.15565,549.03,0.18727,-0.13888,-0.97244,459.55,0.18383,-0.96751,0.17357,376.63,#55,-0.94884,-0.26024,-0.1788,564.7,0.19961,-0.055625,-0.9783,433.85,0.24464,-0.96394,0.10473,380.99,#56,-0.95821,-0.22108,-0.18153,554.52,0.21549,-0.14048,-0.96635,451.66,0.18814,-0.96508,0.18225,375.21,#57,-0.95603,-0.24672,-0.15854,555.57,0.1923,-0.11923,-0.97407,453.47,0.22142,-0.96172,0.16143,370.2

> view matrix models
> #51,-0.95663,-0.23097,-0.17749,561.18,0.20176,-0.085897,-0.97566,442.44,0.21011,-0.96916,0.12877,384.05,#52,-0.96188,-0.22359,-0.15744,556.59,0.18069,-0.087496,-0.97964,448.87,0.20526,-0.97075,0.12456,385.86,#53,-0.95439,-0.24862,-0.16531,557.55,0.19576,-0.10307,-0.97522,448.88,0.22542,-0.9631,0.14704,374.34,#54,-0.9655,-0.21082,-0.15285,548.51,0.18575,-0.14618,-0.97166,461.13,0.1825,-0.96653,0.18029,375.42,#55,-0.94943,-0.26003,-0.17598,564.26,0.19856,-0.063046,-0.97806,435.51,0.24323,-0.96354,0.11149,379.95,#56,-0.95884,-0.22063,-0.17875,554.03,0.21402,-0.1478,-0.96558,453.25,0.18662,-0.9641,0.18893,374.05,#57,-0.95659,-0.24633,-0.15574,555.07,0.19107,-0.12659,-0.97338,455.03,0.22006,-0.96088,0.16816,369.02

> view matrix models
> #51,-0.97658,-0.16476,-0.13833,544.88,0.15235,-0.075648,-0.98543,452.87,0.15189,-0.98343,0.098977,405.03,#52,-0.9805,-0.15722,-0.11789,539.89,0.13116,-0.076866,-0.98838,459.04,0.14633,-0.98457,0.095988,406.66,#53,-0.97503,-0.18191,-0.12736,541.58,0.14613,-0.093756,-0.98481,459.34,0.1672,-0.97884,0.118,395.24,#54,-0.98291,-0.14194,-0.11723,531.91,0.13654,-0.13497,-0.9814,471.13,0.12348,-0.98063,0.15204,395.95,#55,-0.97135,-0.19517,-0.13562,548.55,0.14877,-0.054303,-0.98738,446.18,0.18535,-0.97926,0.081783,401.02,#56,-0.97788,-0.1518,-0.14388,537.88,0.16499,-0.13709,-0.97672,463.55,0.12854,-0.97886,0.15911,394.8,#57,-0.97666,-0.17864,-0.11925,539.14,0.14146,-0.11718,-0.98298,465.48,0.16162,-0.97691,0.13972,389.88

> view matrix models
> #51,-0.97658,-0.16476,-0.13833,532.51,0.15235,-0.075648,-0.98543,455.86,0.15189,-0.98343,0.098977,414.32,#52,-0.9805,-0.15722,-0.11789,527.53,0.13116,-0.076866,-0.98838,462.03,0.14633,-0.98457,0.095988,415.95,#53,-0.97503,-0.18191,-0.12736,529.21,0.14613,-0.093756,-0.98481,462.33,0.1672,-0.97884,0.118,404.53,#54,-0.98291,-0.14194,-0.11723,519.55,0.13654,-0.13497,-0.9814,474.12,0.12348,-0.98063,0.15204,405.24,#55,-0.97135,-0.19517,-0.13562,536.18,0.14877,-0.054303,-0.98738,449.17,0.18535,-0.97926,0.081783,410.31,#56,-0.97788,-0.1518,-0.14388,525.51,0.16499,-0.13709,-0.97672,466.54,0.12854,-0.97886,0.15911,404.09,#57,-0.97666,-0.17864,-0.11925,526.78,0.14146,-0.11718,-0.98298,468.47,0.16162,-0.97691,0.13972,399.17

> view matrix models
> #51,-0.97658,-0.16476,-0.13833,538.43,0.15235,-0.075648,-0.98543,454.9,0.15189,-0.98343,0.098977,403.7,#52,-0.9805,-0.15722,-0.11789,533.44,0.13116,-0.076866,-0.98838,461.07,0.14633,-0.98457,0.095988,405.33,#53,-0.97503,-0.18191,-0.12736,535.12,0.14613,-0.093756,-0.98481,461.36,0.1672,-0.97884,0.118,393.9,#54,-0.98291,-0.14194,-0.11723,525.46,0.13654,-0.13497,-0.9814,473.15,0.12348,-0.98063,0.15204,394.62,#55,-0.97135,-0.19517,-0.13562,542.1,0.14877,-0.054303,-0.98738,448.21,0.18535,-0.97926,0.081783,399.69,#56,-0.97788,-0.1518,-0.14388,531.42,0.16499,-0.13709,-0.97672,465.57,0.12854,-0.97886,0.15911,393.47,#57,-0.97666,-0.17864,-0.11925,532.69,0.14146,-0.11718,-0.98298,467.5,0.16162,-0.97691,0.13972,388.55

> fitmap #51-57 inMap #50 eachModel true

Fit map EMD-12059_PRE1.mrc in map Stable_60S.mrc using 92586 points  
correlation = 0.7934, correlation about mean = 0.2582, overlap = 4659  
steps = 100, shift = 12.8, angle = 12.4 degrees  
  
Position of EMD-12059_PRE1.mrc (#51) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
-0.98786089 0.05094722 -0.14674891 490.89502808  
0.14219287 -0.08380227 -0.98628514 453.72786211  
-0.06254637 -0.99517916 0.07554065 472.94563363  
Axis -0.07145020 -0.67644147 0.73302237  
Axis point 258.78938860 455.52119611 -0.00000000  
Rotation angle (degrees) 176.43164233  
Shift along axis 4.68483789  
  
Fit map EMD-12061_PRE2.mrc in map Stable_60S.mrc using 92518 points  
correlation = 0.8163, correlation about mean = 0.2849, overlap = 4034  
steps = 100, shift = 12.9, angle = 12.4 degrees  
  
Position of EMD-12061_PRE2.mrc (#52) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
-0.99056686 0.05887950 -0.12373554 485.11040210  
0.11848848 -0.08553718 -0.98926430 460.65437686  
-0.06883138 -0.99459368 0.07775375 473.37015044  
Axis -0.06561948 -0.67602328 0.73395273  
Axis point 257.30260947 455.04779684 0.00000000  
Rotation angle (degrees) 177.67268248  
Shift along axis 4.18554103  
  
Fit map EMD-12075_PRE3.mrc in map Stable_60S.mrc using 92602 points  
correlation = 0.8095, correlation about mean = 0.2276, overlap = 3836  
steps = 100, shift = 14, angle = 13.3 degrees  
  
Position of EMD-12075_PRE3.mrc (#53) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
-0.98927874 0.04910268 -0.13753726 489.96845321  
0.13318425 -0.08302087 -0.98760796 456.02314912  
-0.05991266 -0.99533736 0.07559107 471.94840052  
Axis -0.06739066 -0.67678919 0.73308587  
Axis point 257.69361734 455.46023553 0.00000000  
Rotation angle (degrees) 176.71241540  
Shift along axis 4.32786760  
  
Fit map EMD-12065_PRE4.mrc in map Stable_60S.mrc using 92599 points  
correlation = 0.7801, correlation about mean = 0.2357, overlap = 5205  
steps = 104, shift = 16.3, angle = 15 degrees  
  
Position of EMD-12065_PRE4.mrc (#54) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
-0.98930920 0.10238972 -0.10384436 469.53910373  
0.09939131 -0.04768741 -0.99390506 457.11657850  
-0.10671773 -0.99360065 0.03700095 491.26988070  
Axis 0.07310473 0.69004033 -0.72006947  
Axis point 260.03995202 463.60986482 0.00000000  
Rotation angle (degrees) 179.88070824  
Shift along axis -3.99403992  
  
Fit map EMD-12074_POST1.mrc in map Stable_60S.mrc using 92601 points  
correlation = 0.8475, correlation about mean = 0.3496, overlap = 3886  
steps = 128, shift = 10.2, angle = 14.2 degrees  
  
Position of EMD-12074_POST1.mrc (#55) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
-0.98936524 0.04994739 -0.13660774 489.62449946  
0.13206850 -0.08504625 -0.98758546 456.85981594  
-0.06094529 -0.99512431 0.07754533 471.81401672  
Axis -0.06736079 -0.67605584 0.73376497  
Axis point 257.69554811 455.13122069 0.00000000  
Rotation angle (degrees) 176.79212527  
Shift along axis 4.35635748  
  
Fit map EMD-12062_POST2.mrc in map Stable_60S.mrc using 92597 points  
correlation = 0.788, correlation about mean = 0.2194, overlap = 4225  
steps = 100, shift = 14.3, angle = 11.9 degrees  
  
Position of EMD-12062_POST2.mrc (#56) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
-0.98929292 0.04835436 -0.13770027 490.23828165  
0.13330474 -0.08468269 -0.98745060 456.38859992  
-0.05940837 -0.99523399 0.07733012 471.44201648  
Axis -0.06722129 -0.67616821 0.73367421  
Axis point 257.64779039 455.12427442 0.00000000  
Rotation angle (degrees) 176.68107340  
Shift along axis 4.33493733  
  
Fit map EMD-12064_POST3.mrc in map Stable_60S.mrc using 92531 points  
correlation = 0.7863, correlation about mean = 0.2108, overlap = 4146  
steps = 104, shift = 15, angle = 13.3 degrees  
  
Position of EMD-12064_POST3.mrc (#57) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
-0.98930940 0.04856746 -0.13750675 490.15396056  
0.13315352 -0.08370541 -0.98755432 456.20564631  
-0.05947306 -0.99530628 0.07634362 471.68880728  
Axis -0.06720756 -0.67653233 0.73333972  
Axis point 257.65674845 455.32829329 0.00000000  
Rotation angle (degrees) 176.69381433  
Shift along axis 4.32821991  
  

> select clear

> show #!52 models

> hide #!52 models

> show #!52 models

> hide #!52 models

> show #!52 models

> hide #!51 models

> show #!51 models

> hide #!52 models

> hide #!51 models

> ui tool show "Side View"

> show #!51 models

> show #!52 models

> show #!53 models

> show #!54 models

> show #!55 models

> show #!56 models

> show #!57 models

> show #!58 models

> show #!59 models

> show #!60 models

> hide #!60 models

> hide #!59 models

> hide #!58 models

> hide #!57 models

> hide #!56 models

> hide #!55 models

> hide #!54 models

> hide #!53 models

> hide #!52 models

> hide #!51 models

> save
> /Users/campbell/Desktop/Chimera_sessions/Conformationassignment/RotationPDBsandEMDBsCombined.cxs
> includeMaps true

——— End of log from Thu Aug 8 12:51:05 2024 ———

opened ChimeraX session  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/1/MultiPostProcessor_PPout_1.mrc

Opened MultiPostProcessor_PPout_1.mrc as #1, grid size 128,128,128, pixel 4,
shown at level 0.879, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/2/MultiPostProcessor_PPout_2.mrc

Opened MultiPostProcessor_PPout_2.mrc as #2, grid size 128,128,128, pixel 4,
shown at level 0.805, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/3/MultiPostProcessor_PPout_3.mrc

Opened MultiPostProcessor_PPout_3.mrc as #3, grid size 128,128,128, pixel 4,
shown at level 0.833, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/4/MultiPostProcessor_PPout_4.mrc

Opened MultiPostProcessor_PPout_4.mrc as #4, grid size 128,128,128, pixel 4,
shown at level 0.963, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/5/MultiPostProcessor_PPout_5.mrc

Opened MultiPostProcessor_PPout_5.mrc as #5, grid size 128,128,128, pixel 4,
shown at level 0.857, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/6/MultiPostProcessor_PPout_6.mrc

Opened MultiPostProcessor_PPout_6.mrc as #6, grid size 128,128,128, pixel 4,
shown at level 0.868, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/7/MultiPostProcessor_PPout_7.mrc

Opened MultiPostProcessor_PPout_7.mrc as #7, grid size 128,128,128, pixel 4,
shown at level 0.925, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/8/MultiPostProcessor_PPout_8.mrc

Opened MultiPostProcessor_PPout_8.mrc as #8, grid size 128,128,128, pixel 4,
shown at level 0.79, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/9/MultiPostProcessor_PPout_9.mrc

Opened MultiPostProcessor_PPout_9.mrc as #9, grid size 128,128,128, pixel 4,
shown at level 0.95, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/10/MultiPostProcessor_PPout_10.mrc

Opened MultiPostProcessor_PPout_10.mrc as #10, grid size 128,128,128, pixel 4,
shown at level 0.919, step 1, values float32  

> fitmap #1-10 inMap #50 eachModel true

Fit map MultiPostProcessor_PPout_1.mrc in map Stable_60S.mrc using 20970
points  
correlation = 0.8232, correlation about mean = 0.2383, overlap = 1.52e+04  
steps = 148, shift = 2.3, angle = 0.99 degrees  
  
Position of MultiPostProcessor_PPout_1.mrc (#1) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99985148 0.01689255 0.00341564 -3.33682583  
-0.01689673 0.99985652 0.00119912 5.01446636  
-0.00339490 -0.00125666 0.99999345 2.30605403  
Axis -0.07106625 0.19708606 -0.97780707  
Axis point 307.04216643 204.56292077 0.00000000  
Rotation angle (degrees) 0.99001079  
Shift along axis -1.02945885  
  
Fit map MultiPostProcessor_PPout_2.mrc in map Stable_60S.mrc using 20950
points  
correlation = 0.8495, correlation about mean = 0.2183, overlap = 1.345e+04  
steps = 108, shift = 1.59, angle = 0.735 degrees  
  
Position of MultiPostProcessor_PPout_2.mrc (#2) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99999599 0.00218027 -0.00180747 0.40692268  
-0.00220269 0.99991944 -0.01250056 2.06700721  
0.00178007 0.01250449 0.99992023 -3.14881641  
Axis 0.97529261 -0.13992746 -0.17095211  
Axis point 0.00000000 244.07494933 171.01055041  
Rotation angle (degrees) 0.73450957  
Shift along axis 0.64593444  
  
Fit map MultiPostProcessor_PPout_3.mrc in map Stable_60S.mrc using 20949
points  
correlation = 0.8113, correlation about mean = 0.1368, overlap = 1.3e+04  
steps = 60, shift = 1.2, angle = 0.081 degrees  
  
Position of MultiPostProcessor_PPout_3.mrc (#3) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99999928 0.00119593 0.00000657 0.09698330  
-0.00119593 0.99999900 0.00075424 0.73224955  
-0.00000567 -0.00075425 0.99999972 1.14099446  
Axis -0.53344196 0.00433064 -0.84582559  
Axis point 615.64347975 371.40899032 0.00000000  
Rotation angle (degrees) 0.08101171  
Shift along axis -1.01364616  
  
Fit map MultiPostProcessor_PPout_4.mrc in map Stable_60S.mrc using 20960
points  
correlation = 0.8188, correlation about mean = 0.2091, overlap = 1.682e+04  
steps = 116, shift = 2.6, angle = 0.312 degrees  
  
Position of MultiPostProcessor_PPout_4.mrc (#4) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99998550 -0.00421016 -0.00335633 3.25936117  
0.00420754 0.99999084 -0.00078891 0.76712387  
0.00335962 0.00077477 0.99999406 0.48707566  
Axis 0.14370120 -0.61719106 0.77357945  
Axis point -235.18549940 762.28815719 0.00000000  
Rotation angle (degrees) 0.31173326  
Shift along axis 0.37170384  
  
Fit map MultiPostProcessor_PPout_5.mrc in map Stable_60S.mrc using 20966
points  
correlation = 0.818, correlation about mean = 0.2113, overlap = 1.441e+04  
steps = 68, shift = 2.65, angle = 0.436 degrees  
  
Position of MultiPostProcessor_PPout_5.mrc (#5) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99999041 0.00260182 0.00352261 0.01486523  
-0.00262368 0.99997723 0.00621766 0.98420510  
-0.00350635 -0.00622684 0.99997447 3.51546630  
Axis -0.81776603 0.46189442 -0.34338356  
Axis point 0.00000000 523.27015458 -213.18390223  
Rotation angle (degrees) 0.43595863  
Shift along axis -0.76471077  
  
Fit map MultiPostProcessor_PPout_6.mrc in map Stable_60S.mrc using 20958
points  
correlation = 0.8227, correlation about mean = 0.2461, overlap = 1.506e+04  
steps = 84, shift = 2.21, angle = 1.05 degrees  
  
Position of MultiPostProcessor_PPout_6.mrc (#6) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99989672 -0.00490389 -0.01350962 5.54445758  
0.00474986 0.99992362 -0.01140997 2.86381998  
0.01356454 0.01134462 0.99984364 -4.47863636  
Axis 0.62068782 -0.73851477 0.26332978  
Axis point 337.65012800 0.00000000 401.07076604  
Rotation angle (degrees) 1.05029872  
Shift along axis 0.14704558  
  
Fit map MultiPostProcessor_PPout_7.mrc in map Stable_60S.mrc using 20961
points  
correlation = 0.8125, correlation about mean = 0.2052, overlap = 1.615e+04  
steps = 120, shift = 2.42, angle = 1.07 degrees  
  
Position of MultiPostProcessor_PPout_7.mrc (#7) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99982781 0.01829639 0.00309618 -3.59801598  
-0.01830028 0.99983178 0.00123302 5.36311958  
-0.00307310 -0.00128946 0.99999445 2.45369240  
Axis -0.06781110 0.16584717 -0.98381725  
Axis point 302.78964134 204.24728861 0.00000000  
Rotation angle (degrees) 1.06572399  
Shift along axis -1.28054129  
  
Fit map MultiPostProcessor_PPout_8.mrc in map Stable_60S.mrc using 20955
points  
correlation = 0.829, correlation about mean = 0.2004, overlap = 1.263e+04  
steps = 68, shift = 1.88, angle = 0.37 degrees  
  
Position of MultiPostProcessor_PPout_8.mrc (#8) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99999659 -0.00080404 -0.00248558 1.25940033  
0.00081871 0.99998223 0.00590518 0.20456388  
0.00248079 -0.00590720 0.99997948 0.88248004  
Axis -0.91453356 -0.38450487 0.12563583  
Axis point 0.00000000 173.06679830 38.77671696  
Rotation angle (degrees) 0.37002694  
Shift along axis -1.11954857  
  
Fit map MultiPostProcessor_PPout_9.mrc in map Stable_60S.mrc using 20956
points  
correlation = 0.822, correlation about mean = 0.2167, overlap = 1.676e+04  
steps = 116, shift = 2.48, angle = 0.549 degrees  
  
Position of MultiPostProcessor_PPout_9.mrc (#9) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99996878 -0.00512299 -0.00601608 4.12513152  
0.00509034 0.99997230 -0.00543084 1.50305801  
0.00604374 0.00540004 0.99996716 -1.28279790  
Axis 0.56532163 -0.62946664 0.53308836  
Axis point 277.53729146 0.00000000 618.27260090  
Rotation angle (degrees) 0.54886738  
Shift along axis 0.70205658  
  
Fit map MultiPostProcessor_PPout_10.mrc in map Stable_60S.mrc using 20951
points  
correlation = 0.8153, correlation about mean = 0.1922, overlap = 1.604e+04  
steps = 68, shift = 3.11, angle = 0.58 degrees  
  
Position of MultiPostProcessor_PPout_10.mrc (#10) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99998664 -0.00166387 0.00489427 1.02886494  
0.00162118 0.99996072 0.00871367 -0.34077179  
-0.00490858 -0.00870562 0.99995006 4.65054117  
Axis -0.85994281 0.48394006 0.16217391  
Axis point 0.00000000 539.56003047 25.12943779  
Rotation angle (degrees) 0.58031133  
Shift along axis -0.29548171  
  

> hide #!50 models

> show #!50 models

> hide #!50 models

> show #!50 models

> hide #!50 models

> show #!50 models

> hide #!50 models

> volume #1-10 level 0.77

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> volume #1 level 0.5499

> volume #1 level 0.493

> volume #1 level 0.7396

> show #!58 models

> volume #1 level 0.4247

> volume #1 color #b2b2b295

> show #!59 models

> show #!60 models

> hide atoms

> show cartoons

> hide #!59 models

> hide #!60 models

> show #!59 models

> show #!60 models

> hide #!1 models

> color bychain

> color bypolymer

[Repeated 1 time(s)]

> color bychain

> hide #!60 models

> show #!60 models

> hide #!60 models

> hide #!59 models

> show #!59 models

> show #!60 models

> color bychain

> color bypolymer

> color bychain

> hide #!60 models

> show #!60 models

> hide #!59 models

> color #!58,60 bypolymer

> color #!58,60 bychain

> hide #!58 models

> hide #!60 models

> show #!59 models

> color #!59 bypolymer

> show #!58 models

> show #!60 models

> close #1-10

> hide #!59 models

> hide #!60 models

> select #58/1S:1222

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

> select up

37949 atoms, 42445 bonds, 1781 residues, 1 model selected  

> select up

209136 atoms, 224719 bonds, 17082 residues, 1 model selected  

> select down

37949 atoms, 42445 bonds, 1781 residues, 1 model selected  

> color sel cornflower blue

> hide #!58 models

> show #!59 models

> select #59/1S:1222

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

> select up

37949 atoms, 42445 bonds, 1781 residues, 1 model selected  

> color sel orange red

> hide #!59 models

> show #!60 models

> show #!59 models

> color sel #ffc7beff

> color sel #ffcb92ff

> color sel #ff9095ff

> color sel #ff7c88ff

> hide #!59 models

> select #60/18S:1217

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

> select up

36918 atoms, 41291 bonds, 1732 residues, 1 model selected  

> color sel #ffe39dff

> color sel #fbff94ff

> select clear

> show #!59 models

> show #!58 models

> show #!50 models

> hide #!58 models

> hide #!59 models

> hide #!60 models

> save
> /Users/campbell/Desktop/Chimera_sessions/Conformationassignment/RotationPDBsandEMDBsCombined.cxs
> includeMaps true

——— End of log from Thu Aug 8 13:05:51 2024 ———

opened ChimeraX session  

> open 7osa

7osa title:  
Pre-translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands
[more info...]  
  
Chain information for 7osa #1  
---  
Chain | Description | UniProt  
18S | 18S rRNA |   
25S | 25S rRNA |   
58S | 5.8S rRNA |   
AB | 5S |   
PSIT | Psite tRNA-Phe |   
RACK | BJ4_G0022010.mRNA.1.CDS.1 | A0A6L1BKH8_YEASX 1-319  
eEF2 | Elongation factor 2 | A0A6A5Q7K2_YEASX 1-842  
eL13 | 60S ribosomal protein L13 | A0A6L1AF71_YEASX 1-199  
eL14 | 60S ribosomal protein L14-A | RL14A_YEAST 1-138  
eL15 | 60S ribosomal protein L15-A | RL15A_YEAST 1-204  
eL18 | BJ4_G0033900.mRNA.1.CDS.1 | A0A6L1A7F6_YEASX 1-186  
eL19 | 60S ribosomal protein L19-A | RL19A_YEAST 1-189  
eL20 | 60S ribosomal protein L20 | A0A6V8RR03_YEASX 1-172  
eL21 | BJ4_G0003770.mRNA.1.CDS.1 | A0A6L0YTI6_YEASX 1-160  
eL22 | 60S ribosomal protein L22-A | A0A6L0ZZW6_YEASX 1-121  
eL24 | 60S ribosomal protein L24-A | A0A6A5PY83_YEASX 1-155  
eL27 | 60S ribosomal protein L27 | A0A6L0ZQQ7_YEASX 2-136  
eL29 | 60S ribosomal protein L29 | A0A6A5PWR1_YEASX 1-59  
eL30 | BJ4_G0020000.mRNA.1.CDS.1 | A0A6L0ZM08_YEASX 1-105  
eL31 | BJ4_G0008090.mRNA.1.CDS.1 | A0A6L0YFR2_YEASX 1-113  
eL32 | HN1_G0013350.mRNA.1.CDS.1 | A0A7I9CD28_YEASX 1-130  
eL33 | BJ4_G0025510.mRNA.1.CDS.1 | A0A6L1C3H0_YEASX 1-107  
eL34 | 60S ribosomal protein L34-A | A0A6L0ZFW3_YEASX 1-121  
eL36 | 60S ribosomal protein L36-A | RL36A_YEAST 1-100  
eL37 | Ribosomal protein L37 | A0A6L1BIE7_YEASX 1-88  
eL38 | BJ4_G0032190.mRNA.1.CDS.1 | A0A6A5PUL8_YEASX 1-78  
eL39 | 60S ribosomal protein L39 | A0A6L1ASX0_YEASX 1-51  
eL40 | Ubiquitin | A0A6V8S9K0_YEASX 1-128  
eL41 | eL41 |   
eL42 | BJ4_G0001880.mRNA.1.CDS.1 | A0A6L1B5X0_YEASX 1-106  
eL43 | 60S ribosomal protein L43-A | RL43A_YEAST 1-92  
eL6 | 60S ribosomal protein L6 | A0A6L1BLT3_YEASX 1-176  
eL8 | 60S ribosomal protein L8-A | RL8A_YEAST 1-256  
eS1 | 40S ribosomal protein S1 | A0A6A5PRY4_YEASX 1-255  
eS10 | 40S ribosomal protein S10-A | A0A6L0ZM59_YEASX 1-105  
eS12 | 40S ribosomal protein S12 | A0A6A5Q8I3_YEASX 1-143  
eS17 | BJ4_G0020710.mRNA.1.CDS.1 | A0A6L1BLL7_YEASX 1-136  
eS19 | 40S ribosomal protein S19-A | A0A6L1BWT3_YEASX 1-144  
eS21 | 40S ribosomal protein S21 | A0A6L1BDN3_YEASX 1-87  
eS24 | 40S ribosomal protein S24 | A0A6L1AUB6_YEASX 1-135  
eS25 | 40S ribosomal protein S25 | A0A6A5PZ18_YEASX 1-108  
eS26 | 40S ribosomal protein S26 | A0A6A5PUG0_YEASX 1-119  
eS27 | 40S ribosomal protein S27-A | RS27A_YEAST 1-82  
eS28 | eS28 | A0A6A5Q700_YEASX 1-67  
eS30 | 40S ribosomal protein S30 | A0A6L1A1E1_YEASX 1-63  
eS31 | Ubiquitin-40S ribosomal protein S31 | A0A6A5PU37_YEASX 1-152  
eS4 | 40S ribosomal protein S4 | A0A6L0Z3Q0_YEASX 1-261  
eS6 | 40S ribosomal protein S6 | A0A6L1AMY1_YEASX 1-236  
eS7 | 40S ribosomal protein S7 | A0A6L1ACT7_YEASX 1-190  
eS8 | 40S ribosomal protein S8 | A0A6A5Q1H1_YEASX 1-200  
mRNA | MRNA |   
uL10 | 60S acidic ribosomal protein P0 | A0A6A5PT43_YEASX 1-312  
uL11 | 60S ribosomal protein L12-B | A0A6A5Q275_YEASX 1-165  
uL13 | 60S ribosomal protein L16-A | A0A6L0ZD57_YEASX 1-199  
uL14 | 60S ribosomal protein L23-B | A0A6L0Z7E4_YEASX 1-137  
uL15 | 60S ribosomal protein L28 | A0A6L0ZDK5_YEASX 1-149  
uL16 | 60S ribosomal protein L10 | A0A6A5PUZ5_YEASX 1-221  
uL18 | 60S ribosomal protein L5 | A0A6A5Q0W8_YEASX 1-297  
uL2 | 60S ribosomal protein L2-B | A0A6L0Y8L2_YEASX 1-254  
uL22 | BJ4_G0005750.mRNA.1.CDS.1 | A0A6L1BCL1_YEASX 1-184  
uL23 | 60S ribosomal protein L25 | A0A6L0YSM0_YEASX 1-142  
uL24 | 60S ribosomal protein L26-A | RL26A_YEAST 1-127  
uL29 | BJ4_G0044250.mRNA.1.CDS.1 | A0A7I9BRN0_YEASX 1-120  
uL3 | 60S ribosomal protein L3 | A0A6A5Q627_YEASX 1-387  
uL30 | 60S ribosomal protein L7-A | RL7A_YEAST 1-244  
uL4 | BJ4_G0008850.mRNA.1.CDS.1 | A0A6A5Q3W0_YEASX 1-362  
uL5 | BJ4_G0027750.mRNA.1.CDS.1 | A0A6A5Q7I9_YEASX 1-174  
uL6 | 60S ribosomal protein L9-A | RL9A_YEAST 1-191  
uS10 | 40S ribosomal protein S20 | A0A6A5PVE9_YEASX 1-121  
uS11 | 40S ribosomal protein S14-A | A0A6L1AAG7_YEASX 1-137  
uS12 | 40S ribosomal protein S23 | A0A6L1B1T2_YEASX 1-145  
uS13 | 40S ribosomal protein S18-B | A0A6L1AIT6_YEASX 1-146  
uS14 | HLJ1_G0030400.mRNA.1.CDS.1 | A0A6A5PV92_YEASX 1-56  
uS15 | 40S ribosomal protein S13 | A0A6L0YFM5_YEASX 1-151  
uS17 | 40S ribosomal protein S11-B | A0A6L0YMX6_YEASX 1-156  
uS19 | 40S ribosomal protein S15 | A0A6A5Q6F2_YEASX 1-142  
uS2 | 40S ribosomal protein S0 | A0A6L0ZRP4_YEASX 1-252  
uS3 | BJ4_G0045400.mRNA.1.CDS.1 | A0A6L0ZVK6_YEASX 1-240  
uS4 | BJ4_G0026100.mRNA.1.CDS.1 | A0A7I9GPQ3_YEASX 1-197  
uS5 | 40S ribosomal protein S2 | A0A6A5PWF7_YEASX 1-254  
uS7 | Rps5p | A0A1L4AA68_YEASX 1-225  
uS8 | 40S ribosomal protein S22-A | A0A6A5PSE9_YEASX 1-130  
uS9 | BJ4_G0008010.mRNA.1.CDS.1 | A0A6L0YQ58_YEASX 1-143  
  
Non-standard residues in 7osa #1  
---  
GTP — guanosine-5'-triphosphate  
MG — magnesium ion  
ZN — zinc ion  
  
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select #1/eS26:96@CB

1 atom, 1 residue, 1 model selected  

> select #1/eS1:147@O

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,97.06,0,1,0,-68.834,0,0,1,94.457

> view matrix models #1,1,0,0,125.71,0,1,0,-83.844,0,0,1,133.76

> view matrix models
> #1,-0.70441,-0.70086,0.11225,9.1273,0.60532,-0.67576,-0.42064,-21.473,0.37067,-0.22836,0.90025,163.27

> view matrix models
> #1,-0.70669,-0.63072,0.3206,-3.4427,0.54815,-0.77457,-0.31555,-31.532,0.44735,-0.047264,0.89311,168.78

> show #!58 models

> hide #!58 models

> view matrix models
> #1,-0.70669,-0.63072,0.3206,278.62,0.54815,-0.77457,-0.31555,133.5,0.44735,-0.047264,0.89311,127.99

> view matrix models
> #1,-0.70669,-0.63072,0.3206,173.05,0.54815,-0.77457,-0.31555,295.8,0.44735,-0.047264,0.89311,236.76

> fitmap #1 inMap #50

Fit molecule 7osa (#1) to map Stable_60S.mrc (#50) using 208051 atoms  
average map value = 0.541, steps = 168  
shifted from previous position = 11.5  
rotated from previous position = 20.1 degrees  
atoms outside contour = 121624, contour level = 0.78541  
  
Position of 7osa (#1) relative to Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
-0.72595319 -0.45266848 0.51776754 167.80645740  
0.25751860 -0.87699407 -0.40566683 280.60432310  
0.63771165 -0.16116036 0.75322719 247.50008222  
Axis 0.32145878 -0.15769352 0.93370071  
Axis point 7.59184166 170.76745427 0.00000000  
Rotation angle (degrees) 157.64725856  
Shift along axis 240.78437813  
  

> show sel cartoons

> hide sel atoms

[Repeated 1 time(s)]

> show sel cartoons

> select clear

> hide #!1 atoms

> show #!1 cartoons

> show #!58 models

> hide #!58 models

> show #!58 models

> show #!59 models

> show #!60 models

> hide #!60 models

> hide #!59 models

> hide #!58 models

> rename #60 id #61

> rename #1 id #60

> hide #!60 models

> save
> /Users/campbell/Desktop/Chimera_sessions/Conformationassignment/RotationPDBsandEMDBsCombined.cxs
> includeMaps true

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/1/MultiPostProcessor_PPout_1.mrc

Opened MultiPostProcessor_PPout_1.mrc as #1, grid size 128,128,128, pixel 4,
shown at level 0.879, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/2/MultiPostProcessor_PPout_2.mrc

Opened MultiPostProcessor_PPout_2.mrc as #2, grid size 128,128,128, pixel 4,
shown at level 0.805, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/3/MultiPostProcessor_PPout_3.mrc

Opened MultiPostProcessor_PPout_3.mrc as #3, grid size 128,128,128, pixel 4,
shown at level 0.833, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/4/MultiPostProcessor_PPout_4.mrc

Opened MultiPostProcessor_PPout_4.mrc as #4, grid size 128,128,128, pixel 4,
shown at level 0.963, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/5/MultiPostProcessor_PPout_5.mrc

Opened MultiPostProcessor_PPout_5.mrc as #5, grid size 128,128,128, pixel 4,
shown at level 0.857, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/6/MultiPostProcessor_PPout_6.mrc

Opened MultiPostProcessor_PPout_6.mrc as #6, grid size 128,128,128, pixel 4,
shown at level 0.868, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/7/MultiPostProcessor_PPout_7.mrc

Opened MultiPostProcessor_PPout_7.mrc as #7, grid size 128,128,128, pixel 4,
shown at level 0.925, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/8/MultiPostProcessor_PPout_8.mrc

Opened MultiPostProcessor_PPout_8.mrc as #8, grid size 128,128,128, pixel 4,
shown at level 0.79, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/9/MultiPostProcessor_PPout_9.mrc

Opened MultiPostProcessor_PPout_9.mrc as #9, grid size 128,128,128, pixel 4,
shown at level 0.95, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/1_tRNA_T6/10/MultiPostProcessor_PPout_10.mrc

Opened MultiPostProcessor_PPout_10.mrc as #10, grid size 128,128,128, pixel 4,
shown at level 0.919, step 1, values float32  

> fitmap #1-10 inMap #50 eachModel true

Fit map MultiPostProcessor_PPout_1.mrc in map Stable_60S.mrc using 20970
points  
correlation = 0.8232, correlation about mean = 0.2383, overlap = 1.52e+04  
steps = 148, shift = 2.3, angle = 0.99 degrees  
  
Position of MultiPostProcessor_PPout_1.mrc (#1) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99985148 0.01689255 0.00341564 -3.33682583  
-0.01689673 0.99985652 0.00119912 5.01446636  
-0.00339490 -0.00125666 0.99999345 2.30605403  
Axis -0.07106625 0.19708606 -0.97780707  
Axis point 307.04216643 204.56292077 0.00000000  
Rotation angle (degrees) 0.99001079  
Shift along axis -1.02945885  
  
Fit map MultiPostProcessor_PPout_2.mrc in map Stable_60S.mrc using 20950
points  
correlation = 0.8495, correlation about mean = 0.2183, overlap = 1.345e+04  
steps = 108, shift = 1.59, angle = 0.735 degrees  
  
Position of MultiPostProcessor_PPout_2.mrc (#2) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99999599 0.00218027 -0.00180747 0.40692268  
-0.00220269 0.99991944 -0.01250056 2.06700721  
0.00178007 0.01250449 0.99992023 -3.14881641  
Axis 0.97529261 -0.13992746 -0.17095211  
Axis point 0.00000000 244.07494933 171.01055041  
Rotation angle (degrees) 0.73450957  
Shift along axis 0.64593444  
  
Fit map MultiPostProcessor_PPout_3.mrc in map Stable_60S.mrc using 20949
points  
correlation = 0.8113, correlation about mean = 0.1368, overlap = 1.3e+04  
steps = 60, shift = 1.2, angle = 0.081 degrees  
  
Position of MultiPostProcessor_PPout_3.mrc (#3) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99999928 0.00119593 0.00000657 0.09698330  
-0.00119593 0.99999900 0.00075424 0.73224955  
-0.00000567 -0.00075425 0.99999972 1.14099446  
Axis -0.53344196 0.00433064 -0.84582559  
Axis point 615.64347975 371.40899032 0.00000000  
Rotation angle (degrees) 0.08101171  
Shift along axis -1.01364616  
  
Fit map MultiPostProcessor_PPout_4.mrc in map Stable_60S.mrc using 20960
points  
correlation = 0.8188, correlation about mean = 0.2091, overlap = 1.682e+04  
steps = 116, shift = 2.6, angle = 0.312 degrees  
  
Position of MultiPostProcessor_PPout_4.mrc (#4) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99998550 -0.00421016 -0.00335633 3.25936117  
0.00420754 0.99999084 -0.00078891 0.76712387  
0.00335962 0.00077477 0.99999406 0.48707566  
Axis 0.14370120 -0.61719106 0.77357945  
Axis point -235.18549940 762.28815719 0.00000000  
Rotation angle (degrees) 0.31173326  
Shift along axis 0.37170384  
  
Fit map MultiPostProcessor_PPout_5.mrc in map Stable_60S.mrc using 20966
points  
correlation = 0.818, correlation about mean = 0.2113, overlap = 1.441e+04  
steps = 68, shift = 2.65, angle = 0.436 degrees  
  
Position of MultiPostProcessor_PPout_5.mrc (#5) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99999041 0.00260182 0.00352261 0.01486523  
-0.00262368 0.99997723 0.00621766 0.98420510  
-0.00350635 -0.00622684 0.99997447 3.51546630  
Axis -0.81776603 0.46189442 -0.34338356  
Axis point 0.00000000 523.27015458 -213.18390223  
Rotation angle (degrees) 0.43595863  
Shift along axis -0.76471077  
  
Fit map MultiPostProcessor_PPout_6.mrc in map Stable_60S.mrc using 20958
points  
correlation = 0.8227, correlation about mean = 0.2461, overlap = 1.506e+04  
steps = 84, shift = 2.21, angle = 1.05 degrees  
  
Position of MultiPostProcessor_PPout_6.mrc (#6) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99989672 -0.00490389 -0.01350962 5.54445758  
0.00474986 0.99992362 -0.01140997 2.86381998  
0.01356454 0.01134462 0.99984364 -4.47863636  
Axis 0.62068782 -0.73851477 0.26332978  
Axis point 337.65012800 0.00000000 401.07076604  
Rotation angle (degrees) 1.05029872  
Shift along axis 0.14704558  
  
Fit map MultiPostProcessor_PPout_7.mrc in map Stable_60S.mrc using 20961
points  
correlation = 0.8125, correlation about mean = 0.2052, overlap = 1.615e+04  
steps = 120, shift = 2.42, angle = 1.07 degrees  
  
Position of MultiPostProcessor_PPout_7.mrc (#7) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99982781 0.01829639 0.00309618 -3.59801598  
-0.01830028 0.99983178 0.00123302 5.36311958  
-0.00307310 -0.00128946 0.99999445 2.45369240  
Axis -0.06781110 0.16584717 -0.98381725  
Axis point 302.78964134 204.24728861 0.00000000  
Rotation angle (degrees) 1.06572399  
Shift along axis -1.28054129  
  
Fit map MultiPostProcessor_PPout_8.mrc in map Stable_60S.mrc using 20955
points  
correlation = 0.829, correlation about mean = 0.2004, overlap = 1.263e+04  
steps = 68, shift = 1.88, angle = 0.37 degrees  
  
Position of MultiPostProcessor_PPout_8.mrc (#8) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99999659 -0.00080404 -0.00248558 1.25940033  
0.00081871 0.99998223 0.00590518 0.20456388  
0.00248079 -0.00590720 0.99997948 0.88248004  
Axis -0.91453356 -0.38450487 0.12563583  
Axis point 0.00000000 173.06679830 38.77671696  
Rotation angle (degrees) 0.37002694  
Shift along axis -1.11954857  
  
Fit map MultiPostProcessor_PPout_9.mrc in map Stable_60S.mrc using 20956
points  
correlation = 0.822, correlation about mean = 0.2167, overlap = 1.676e+04  
steps = 116, shift = 2.48, angle = 0.549 degrees  
  
Position of MultiPostProcessor_PPout_9.mrc (#9) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99996878 -0.00512299 -0.00601608 4.12513152  
0.00509034 0.99997230 -0.00543084 1.50305801  
0.00604374 0.00540004 0.99996716 -1.28279790  
Axis 0.56532163 -0.62946664 0.53308836  
Axis point 277.53729146 0.00000000 618.27260090  
Rotation angle (degrees) 0.54886738  
Shift along axis 0.70205658  
  
Fit map MultiPostProcessor_PPout_10.mrc in map Stable_60S.mrc using 20951
points  
correlation = 0.8153, correlation about mean = 0.1922, overlap = 1.604e+04  
steps = 68, shift = 3.11, angle = 0.58 degrees  
  
Position of MultiPostProcessor_PPout_10.mrc (#10) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99998664 -0.00166387 0.00489427 1.02886494  
0.00162118 0.99996072 0.00871367 -0.34077179  
-0.00490858 -0.00870562 0.99995006 4.65054117  
Axis -0.85994281 0.48394006 0.16217391  
Axis point 0.00000000 539.56003047 25.12943779  
Rotation angle (degrees) 0.58031133  
Shift along axis -0.29548171  
  

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> hide #!50 models

> show #!52 models

> hide #!1 models

> hide #!52 models

> show #!50 models

> close #1-10

> show #!51 models

> volume #51-57 level 0.03

> hide #!51 models

> show #!54 models

> hide #!54 models

> save
> /Users/campbell/Desktop/Chimera_sessions/Conformationassignment/RotationPDBsandEMDBsCombined.cxs
> includeMaps true

——— End of log from Thu Aug 8 16:15:28 2024 ———

opened ChimeraX session  

> volume #50 level 0.6089

> volume #50 level 0.6

> show #!59 models

> hide #!59 models

> save
> /Users/campbell/Desktop/Chimera_sessions/Conformationassignment/RotationPDBsandEMDBsCombined.cxs
> includeMaps true

——— End of log from Fri Aug 9 12:43:00 2024 ———

opened ChimeraX session  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/62_tRNA_AP_T4_correctedmask/9/MultiPostProcessor_PPout_9.mrc

Opened MultiPostProcessor_PPout_9.mrc as #1, grid size 128,128,128, pixel 4,
shown at level 0.971, step 1, values float32  

> volume #1 level 0.6

> fitmap #1 inMap #50

Fit map MultiPostProcessor_PPout_9.mrc in map Stable_60S.mrc using 63729
points  
correlation = 0.7934, correlation about mean = 0.3786, overlap = 3.274e+04  
steps = 60, shift = 0.195, angle = 0.472 degrees  
  
Position of MultiPostProcessor_PPout_9.mrc (#1) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99997099 -0.00689546 -0.00323670 2.40371084  
0.00688528 0.99997135 -0.00314441 -0.74270626  
0.00325829 0.00312203 0.99998982 -1.62795132  
Axis 0.38040546 -0.39427904 0.83656185  
Axis point 118.20917088 356.62844856 0.00000000  
Rotation angle (degrees) 0.47192395  
Shift along axis -0.15466373  
  

> color #1 #bbbbbbff models

> hide #!50 models

> show #!50 models

> hide #!50 models

> lighting soft

> show #!58 models

> hide #!1 models

> hide #!58 models

> show #!59 models

> show #!60 models

> hide #!59 models

> show #!61 models

> hide #!60 models

Drag select of 2699 residues, 4 pseudobonds  

> log metadata #58

No models had metadata

> log chains #58

Chain information for 3j78 #58  
---  
Chain | Description | UniProt  
10 | 40S ribosomal protein S10 | RS10A_YEAST 1-105  
11 | 40S ribosomal protein S11 | RS11A_YEAST 1-156  
12 | 40S ribosomal protein S12 | RS12_YEAST 1-143  
13 | 40S ribosomal protein S13 | RS13_YEAST 1-151  
14 | 40S ribosomal protein S14 | RS14A_YEAST 1-137  
15 | 40S ribosomal protein S15 | RS15_YEAST 1-142  
16 | 40S ribosomal protein S16 | RS16A_YEAST 1-143  
17 | 40S ribosomal protein S17 | RS17A_YEAST 1-136  
18 | 40S ribosomal protein S18 | RS18A_YEAST 1-146  
19 | 40S ribosomal protein S19 | RS19A_YEAST 1-144  
1S | 18S ribosomal RNA |   
20 | 40S ribosomal protein S20 | RS20_YEAST 1-121  
21 | 40S ribosomal protein S21 | RS21A_YEAST 1-87  
22 | 40S ribosomal protein S22 | RS22A_YEAST 1-130  
23 | 40S ribosomal protein S23 | RS23A_YEAST 1-145  
24 | 40S ribosomal protein S24 | RS24A_YEAST 1-135  
25 | 40S ribosomal protein S25 | RS25A_YEAST 1-108  
26 | 40S ribosomal protein S26 | RS26A_YEAST 1-119  
27 | 40S ribosomal protein S27 | RS27_YEAST 1-82  
28 | 40S ribosomal protein S28 | RS28A_YEAST 1-67  
29 | 40S ribosomal protein S29 | RS29A_YEAST 1-56  
2S | 25S ribosomal RNA |   
30 | 40S ribosomal protein S30 | RS30A_YEAST 1-63  
31 | 40S ribosomal protein S31 | RS27A_YEAST 1-152  
5S | 5S ribosomal RNA |   
60 | 60S ribosomal protein L10 | RL10_YEAST 1-221  
61 | 60S ribosomal protein L11 | RL11A_YEAST 1-174  
62 | 60S ribosomal protein L12 | RL12A_YEAST 1-165  
63 | 60S ribosomal protein L13 | RL13A_YEAST 1-199  
64 | 60S ribosomal protein L14 | RL14A_YEAST 1-138  
65 | 60S ribosomal protein L15 | RL15A_YEAST 1-204  
66 | 60S ribosomal protein L16 | RL16A_YEAST 1-199  
67 | 60S ribosomal protein L17 | RL17A_YEAST 1-184  
68 | 60S ribosomal protein L18 | RL18A_YEAST 1-186  
69 | 60S ribosomal protein L19 | RL19A_YEAST 1-189  
70 | 60S ribosomal protein L20 | RL20A_YEAST 1-172  
71 | 60S ribosomal protein L21 | RL21A_YEAST 1-160  
72 | 60S ribosomal protein L22 | RL22A_YEAST 1-121  
73 | 60S ribosomal protein L23 | RL23A_YEAST 1-137  
74 | 60S ribosomal protein L24 | RL24A_YEAST 1-155  
75 | 60S ribosomal protein L25 | RL25_YEAST 1-142  
76 | 60S ribosomal protein L26 | RL26A_YEAST 1-127  
77 | 60S ribosomal protein L27 | RL27A_YEAST 1-136  
78 | 60S ribosomal protein L28 | RL28_YEAST 1-149  
79 | 60S ribosomal protein L29 | RL29_YEAST 1-59  
80 | 60S ribosomal protein L30 | RL30_YEAST 1-105  
81 | 60S ribosomal protein L31 | RL31A_YEAST 1-113  
82 | 60S ribosomal protein L32 | RL32_YEAST 1-130  
83 | 60S ribosomal protein L33 | RL33A_YEAST 1-107  
84 | 60S ribosomal protein L34 | RL34A_YEAST 1-121  
85 | 60S ribosomal protein L35 | RL35A_YEAST 1-120  
86 | 60S ribosomal protein L36 | RL36A_YEAST 1-100  
87 | 60S ribosomal protein L37 | RL37A_YEAST 1-88  
88 | 60S ribosomal protein L38 | RL38_YEAST 1-78  
89 | 60S ribosomal protein L39 | RL39_YEAST 1-51  
8S | 5.8S ribosomal RNA |   
90 | 60S ribosomal protein L40 | RL401_YEAST 1-128  
91 | 60S ribosomal protein L41 | RL41A_YEAST 1-25  
92 | 60S ribosomal protein L42 | RL44A_YEAST 1-106  
93 | 60S ribosomal protein L43 | RL43A_YEAST 1-92  
ET PT | P/E-site initiator transfer RNAfMet |   
L1 | 60S ribosomal protein L1 | RL1A_YEAST 1-217  
L2 | 60S ribosomal protein L2 | RL2A_YEAST 1-254  
L3 | 60S ribosomal protein L3 | RL3_YEAST 1-387  
L4 | 60S ribosomal protein L4 | RL4A_YEAST 1-362  
L5 | 60S ribosomal protein L5 | RL5_YEAST 1-297  
L6 | 60S ribosomal protein L6 | RL6A_YEAST 1-176  
L7 | 60S ribosomal protein L7 | RL7A_YEAST 1-244  
L8 | 60S ribosomal protein L8 | RL8A_YEAST 1-256  
L9 | 60S ribosomal protein L9 | RL9A_YEAST 1-191  
MR | messenger RNA |   
P0 | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-312  
RC | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 1-319  
S0 | 40S ribosomal protein S0 | RSSA1_YEAST 1-252  
S1 | 40S ribosomal protein S1 | RS3A1_YEAST 1-255  
S2 | 40S ribosomal protein S2 | RS2_YEAST 1-254  
S3 | 40S ribosomal protein S3 | RS3_YEAST 1-240  
S4 | 40S ribosomal protein S4 | RS4A_YEAST 1-261  
S5 | 40S ribosomal protein S5 | RS5_YEAST 1-225  
S6 | 40S ribosomal protein S6 | RS6A_YEAST 1-236  
S7 | 40S ribosomal protein S7 | RS7A_YEAST 1-190  
S8 | 40S ribosomal protein S8 | RS8A_YEAST 1-200  
S9 | 40S ribosomal protein S9 | RS9A_YEAST 1-197  
  

> select clear

> select #58/5S:1-121

2580 atoms, 2884 bonds, 107 pseudobonds, 121 residues, 2 models selected  

> sequence chain #58/5S

Alignment identifier is 58/5S  

> select #58/5S:1-121

2580 atoms, 2884 bonds, 107 pseudobonds, 121 residues, 2 models selected  

> log metadata #61

No models had metadata

> log chains #61

Chain information for 7osm #61  
---  
Chain | Description | UniProt  
18S | 18S rRNA |   
25S | 25S rRNA |   
58S | 5.8S rRNA |   
AB | 5S rRNA |   
ASIT | PHE tRNA |   
PSIT | FMET tRNA |   
RACK | BJ4_G0022010.mRNA.1.CDS.1 | A0A6L1BKH8_YEASX 1-319  
eEF2 | Elongation factor 2 | A0A6A5Q7K2_YEASX 1-842  
eL13 | 60S ribosomal protein L13 | A0A6L1AF71_YEASX 1-199  
eL14 | 60S ribosomal protein L14-A | RL14A_YEAST 1-138  
eL15 | 60S ribosomal protein L15-A | RL15A_YEAST 1-204  
eL18 | BJ4_G0033900.mRNA.1.CDS.1 | A0A6L1A7F6_YEASX 1-186  
eL19 | 60S ribosomal protein L19-A | RL19A_YEAST 1-189  
eL20 | 60S ribosomal protein L20 | A0A6V8RR03_YEASX 1-172  
eL21 | BJ4_G0003770.mRNA.1.CDS.1 | A0A6L0YTI6_YEASX 1-160  
eL22 | 60S ribosomal protein L22-A | A0A6L0ZZW6_YEASX 1-121  
eL24 | 60S ribosomal protein L24-A | A0A6A5PY83_YEASX 1-155  
eL27 | 60S ribosomal protein L27 | A0A6L0ZQQ7_YEASX 1-136  
eL29 | 60S ribosomal protein L29 | A0A6A5PWR1_YEASX 1-59  
eL30 | BJ4_G0020000.mRNA.1.CDS.1 | A0A6L0ZM08_YEASX 1-105  
eL31 | BJ4_G0008090.mRNA.1.CDS.1 | A0A6L0YFR2_YEASX 1-113  
eL32 | HN1_G0013350.mRNA.1.CDS.1 | A0A7I9CD28_YEASX 1-130  
eL33 | BJ4_G0025510.mRNA.1.CDS.1 | A0A6L1C3H0_YEASX 1-107  
eL34 | 60S ribosomal protein L34-A | A0A6L0ZFW3_YEASX 1-121  
eL36 | 60S ribosomal protein L36-A | RL36A_YEAST 1-100  
eL37 | Ribosomal protein L37 | A0A6L1BIE7_YEASX 1-88  
eL38 | BJ4_G0032190.mRNA.1.CDS.1 | A0A6A5PUL8_YEASX 1-78  
eL39 | 60S ribosomal protein L39 | A0A6L1ASX0_YEASX 1-51  
eL40 | Ubiquitin | A0A6V8S9K0_YEASX 1-128  
eL41 | eL41 |   
eL42 | BJ4_G0001880.mRNA.1.CDS.1 | A0A6L1B5X0_YEASX 1-106  
eL43 | 60S ribosomal protein L43-A | RL43A_YEAST 1-92  
eL6 | 60S ribosomal protein L6 | A0A6L1BLT3_YEASX 1-176  
eL8 | 60S ribosomal protein L8-A | RL8A_YEAST 1-256  
eS1 | 40S ribosomal protein S1 | A0A6A5PRY4_YEASX 1-255  
eS10 | 40S ribosomal protein S10-A | A0A6L0ZM59_YEASX 1-105  
eS17 | BJ4_G0020710.mRNA.1.CDS.1 | A0A6L1BLL7_YEASX 1-136  
eS19 | 40S ribosomal protein S19-A | A0A6L1BWT3_YEASX 1-144  
eS21 | 40S ribosomal protein S21 | A0A6L1BDN3_YEASX 1-87  
eS24 | 40S ribosomal protein S24 | A0A6L1AUB6_YEASX 1-135  
eS25 | 40S ribosomal protein S25 | A0A6A5PZ18_YEASX 1-108  
eS26 | 40S ribosomal protein S26 | A0A6A5PUG0_YEASX 1-119  
eS27 | 40S ribosomal protein S27-A | RS27A_YEAST 1-82  
eS28 | eS28 | A0A6A5Q700_YEASX 1-67  
eS30 | 40S ribosomal protein S30 | A0A6L1A1E1_YEASX 1-63  
eS31 | Ubiquitin-40S ribosomal protein S31 | A0A6A5PU37_YEASX 1-152  
eS4 | 40S ribosomal protein S4 | A0A6L0Z3Q0_YEASX 1-261  
eS6 | 40S ribosomal protein S6 | A0A6L1AMY1_YEASX 1-236  
eS7 | 40S ribosomal protein S7 | A0A6L1ACT7_YEASX 1-190  
eS8 | 40S ribosomal protein S8 | A0A6A5Q1H1_YEASX 1-200  
mRNA | MRNA |   
uL10 | 60S acidic ribosomal protein P0 | A0A6A5PT43_YEASX 1-312  
uL11 | 60S ribosomal protein L12-B | A0A6A5Q275_YEASX 1-165  
uL13 | 60S ribosomal protein L16-A | A0A6L0ZD57_YEASX 1-199  
uL14 | 60S ribosomal protein L23-B | A0A6L0Z7E4_YEASX 1-137  
uL15 | 60S ribosomal protein L28 | A0A6L0ZDK5_YEASX 1-149  
uL16 | 60S ribosomal protein L10 | A0A6A5PUZ5_YEASX 1-221  
uL18 | 60S ribosomal protein L5 | A0A6A5Q0W8_YEASX 1-297  
uL2 | 60S ribosomal protein L2-B | A0A6L0Y8L2_YEASX 1-254  
uL22 | BJ4_G0005750.mRNA.1.CDS.1 | A0A6L1BCL1_YEASX 1-184  
uL23 | 60S ribosomal protein L25 | A0A6L0YSM0_YEASX 1-142  
uL24 | 60S ribosomal protein L26-A | RL26A_YEAST 1-127  
uL29 | BJ4_G0044250.mRNA.1.CDS.1 | A0A7I9BRN0_YEASX 1-120  
uL3 | 60S ribosomal protein L3 | A0A6A5Q627_YEASX 1-387  
uL30 | 60S ribosomal protein L7-A | A0A6V8RJA7_YEASX 1-244  
uL4 | BJ4_G0008850.mRNA.1.CDS.1 | A0A6A5Q3W0_YEASX 1-362  
uL5 | BJ4_G0027750.mRNA.1.CDS.1 | A0A6A5Q7I9_YEASX 1-174  
uL6 | 60S ribosomal protein L9-A | RL9A_YEAST 1-191  
uS10 | 40S ribosomal protein S20 | A0A6A5PVE9_YEASX 1-121  
uS11 | 40S ribosomal protein S14-A | A0A6L1AAG7_YEASX 1-137  
uS12 | 40S ribosomal protein S23 | A0A6L1B1T2_YEASX 1-145  
uS13 | 40S ribosomal protein S18-B | A0A6L1AIT6_YEASX 1-146  
uS14 | HLJ1_G0030400.mRNA.1.CDS.1 | A0A6A5PV92_YEASX 1-56  
uS15 | 40S ribosomal protein S13 | A0A6L0YFM5_YEASX 1-151  
uS17 | 40S ribosomal protein S11-B | A0A6L0YMX6_YEASX 1-156  
uS19 | 40S ribosomal protein S15 | A0A6A5Q6F2_YEASX 1-142  
uS2 | 40S ribosomal protein S0 | A0A6L0ZRP4_YEASX 1-252  
uS3 | BJ4_G0045400.mRNA.1.CDS.1 | A0A6L0ZVK6_YEASX 1-240  
uS4 | BJ4_G0026100.mRNA.1.CDS.1 | A0A7I9GPQ3_YEASX 1-197  
uS5 | 40S ribosomal protein S2 | A0A6A5PWF7_YEASX 1-254  
uS7 | Rps5p | A0A1L4AA68_YEASX 1-225  
uS8 | 40S ribosomal protein S22-A | A0A6A5PSE9_YEASX 1-130  
uS9 | BJ4_G0008010.mRNA.1.CDS.1 | A0A6L0YQ58_YEASX 1-143  
  
Drag select of 2187 residues, 5 pseudobonds  

> select up

53529 atoms, 58170 bonds, 5 pseudobonds, 3849 residues, 2 models selected  

> select up

60691 atoms, 65473 bonds, 5 pseudobonds, 4754 residues, 2 models selected  

> select up

60820 atoms, 65473 bonds, 5 pseudobonds, 4883 residues, 2 models selected  

> select add #61/eS8:192

60832 atoms, 65485 bonds, 5 pseudobonds, 4884 residues, 2 models selected  

> select add #61/eS6:40

60837 atoms, 65489 bonds, 5 pseudobonds, 4885 residues, 2 models selected  

> select add #61/eS6:209

60842 atoms, 65493 bonds, 5 pseudobonds, 4886 residues, 2 models selected  

> select add #61/eS24:79

60849 atoms, 65499 bonds, 5 pseudobonds, 4887 residues, 2 models selected  

> select up

61346 atoms, 66000 bonds, 5 pseudobonds, 4948 residues, 2 models selected  

> select up

64139 atoms, 68837 bonds, 5 pseudobonds, 5298 residues, 2 models selected  

> select up

64202 atoms, 68901 bonds, 5 pseudobonds, 5306 residues, 2 models selected  

> select up

65116 atoms, 69832 bonds, 5 pseudobonds, 5420 residues, 2 models selected  

> select up

65118 atoms, 69832 bonds, 5 pseudobonds, 5422 residues, 2 models selected  

> select up

207066 atoms, 221714 bonds, 28 pseudobonds, 17603 residues, 2 models selected  

> select down

65118 atoms, 69832 bonds, 5 pseudobonds, 5422 residues, 2 models selected  

> select add #61/eS26:54

65124 atoms, 69837 bonds, 5 pseudobonds, 5423 residues, 2 models selected  

> select add #61/eS26:29

65130 atoms, 69842 bonds, 5 pseudobonds, 5424 residues, 2 models selected  

> select up

65199 atoms, 69912 bonds, 5 pseudobonds, 5433 residues, 2 models selected  

> select up

65868 atoms, 70593 bonds, 5 pseudobonds, 5516 residues, 2 models selected  

> select add #61/uS11:65

65873 atoms, 70597 bonds, 5 pseudobonds, 5517 residues, 2 models selected  

> select up

65941 atoms, 70666 bonds, 5 pseudobonds, 5530 residues, 2 models selected  

> select up

66759 atoms, 71494 bonds, 5 pseudobonds, 5643 residues, 2 models selected  

> select up

66761 atoms, 71494 bonds, 5 pseudobonds, 5645 residues, 2 models selected  

> select up

207066 atoms, 221714 bonds, 28 pseudobonds, 17603 residues, 2 models selected  

> select down

66761 atoms, 71494 bonds, 5 pseudobonds, 5645 residues, 2 models selected  

> color (#!61 & sel) yellow

> color (#!61 & sel) #f2ffbcff

> color (#!61 & sel) #ffffa6ff

> color (#!61 & sel) #ffffa5ff

> color (#!61 & sel) #feff86ff

> color (#!61 & sel) #f2ff71ff

> color (#!61 & sel) yellow

> select clear

> select add /*S*

551081 atoms, 605265 bonds, 18511 pseudobonds, 34745 residues, 14 models
selected  

> select /eS*

33073 atoms, 33567 bonds, 21 pseudobonds, 4183 residues, 6 models selected  

> select add /uS*

67393 atoms, 68467 bonds, 38 pseudobonds, 8578 residues, 6 models selected  

> select add #61/18S:495

67413 atoms, 68488 bonds, 38 pseudobonds, 8579 residues, 6 models selected  

> select up

104311 atoms, 109758 bonds, 38 pseudobonds, 10310 residues, 6 models selected  

> select up

104433 atoms, 109758 bonds, 38 pseudobonds, 10432 residues, 6 models selected  

> select up

415117 atoms, 444276 bonds, 996 pseudobonds, 35471 residues, 6 models selected  

> select down

104433 atoms, 109758 bonds, 38 pseudobonds, 10432 residues, 6 models selected  

> color (#!61 & sel) yellow

> name frozen 40S sel

Not registering illegal selector name "40S"  

> Name frozen ssu

Unknown command: Name frozen ssu  

> name frozen ssu

Missing or invalid "objects" argument: empty atom specifier  

> name frozen sel ssu

Missing or invalid "objects" argument: invalid objects specifier  

> name frozen ssu sel

> select ~sel & ##selected

310684 atoms, 334518 bonds, 8685 pseudobonds, 25039 residues, 8 models
selected  

> select subtract /eEF2

297482 atoms, 321070 bonds, 8672 pseudobonds, 23343 residues, 8 models
selected  

> select subtract /*SIT

292549 atoms, 315571 bonds, 8478 pseudobonds, 23104 residues, 8 models
selected  

> color (#!61 & sel) cornflower blue

> select #61/ASIT:17

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

> select add #61/PSIT:54

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select up

3280 atoms, 3663 bonds, 153 residues, 1 model selected  

> select up

3287 atoms, 3663 bonds, 160 residues, 1 model selected  

> color sel purple

> color sel magenta

> color sel #caa4daff

> select #61/eEF2:622

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

> select ssu

104433 atoms, 109758 bonds, 1519 pseudobonds, 10432 residues, 7 models
selected  

> color (#!61 & sel) #fffc79ff

> select ~sel & ##selected

310684 atoms, 334518 bonds, 8685 pseudobonds, 25039 residues, 8 models
selected  

> color (#!61 & sel) #76d6ffff

> select #61/ASIT:44

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #61/PSIT:46

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select up

3280 atoms, 3663 bonds, 153 residues, 1 model selected  

> select up

3287 atoms, 3663 bonds, 160 residues, 1 model selected  

> color sel #ff9300ff

> color sel #ffd479ff

> color sel #ff9300ff

> color sel orange

> color sel orange red

> select #61/eEF2:589

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

> select up

62 atoms, 62 bonds, 7 residues, 1 model selected  

> select up

6569 atoms, 6695 bonds, 842 residues, 1 model selected  

> color sel forest green

> select clear

[Repeated 1 time(s)]

> select ssu

104433 atoms, 109758 bonds, 1519 pseudobonds, 10432 residues, 7 models
selected  

> select add #61/RACK:254

104438 atoms, 109762 bonds, 1519 pseudobonds, 10433 residues, 7 models
selected  

> select up

104455 atoms, 109779 bonds, 1519 pseudobonds, 10436 residues, 7 models
selected  

> select up

106869 atoms, 112247 bonds, 1519 pseudobonds, 10750 residues, 7 models
selected  

> color (#!61 & sel) #fffc79ff

> select clear

> show #!1 models

> volume #1 level 0.77

> volume #1 level 0.7

> volume #1 level 0.77

> ui tool show "Color Zone"

> color zone #1 near #61 distance 4

> color zone #1 near #61 distance 8

[Repeated 1 time(s)]

> color zone #1 near #61 distance 20

[Repeated 2 time(s)]

> save /Users/campbell/Desktop/Chimera_sessions/subunit_colouring.cxs
> includeMaps true

> volume #1 level 0.6992

> volume #1 level 0.7

> lighting simple

> lighting soft

> set bgColor white

> hide #!61 models

> show #!61 models

> select #61/PSIT:53

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #61/ASIT:44

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select up

3280 atoms, 3663 bonds, 153 residues, 1 model selected  

> select up

3287 atoms, 3663 bonds, 160 residues, 1 model selected  

> select up

207066 atoms, 221714 bonds, 17603 residues, 1 model selected  

> select down

3287 atoms, 3663 bonds, 160 residues, 1 model selected  

> color sel #76d6ffff

> color zone #1 near #61 distance 20

> select #61/PSIT:53

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1644 atoms, 1836 bonds, 77 residues, 1 model selected  

> select up

1650 atoms, 1836 bonds, 83 residues, 1 model selected  

> color sel #ff7e79ff

> color zone #1 near #61 distance 4

> color zone #1 near #61 distance 20

> color zone #1 near sel distance 4

> color zone #1 near sel distance 20

> color zone #1 near #61 distance 20

[Repeated 1 time(s)]

> select clear

No atoms selected for color zoning  

[Repeated 1 time(s)]

> hide #!61 models

> show #!61 models

> select #61/PSIT:71

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1644 atoms, 1836 bonds, 77 residues, 1 model selected  

> select up

1650 atoms, 1836 bonds, 83 residues, 1 model selected  

> color sel orange red

> color zone #1 near sel distance 4

> undo

> select clear

No atoms selected for color zoning  

> color zone #1 near #61 distance 20

> show #!59 models

> hide #!61 models

> hide #!1 models

> log metadata #59

No models had metadata

> log chains #59

Chain information for 3j77 #59  
---  
Chain | Description | UniProt  
10 | 40S ribosomal protein S10 | RS10A_YEAST 1-105  
11 | 40S ribosomal protein S11 | RS11A_YEAST 1-156  
12 | 40S ribosomal protein S12 | RS12_YEAST 1-143  
13 | 40S ribosomal protein S13 | RS13_YEAST 1-151  
14 | 40S ribosomal protein S14 | RS14A_YEAST 1-137  
15 | 40S ribosomal protein S15 | RS15_YEAST 1-142  
16 | 40S ribosomal protein S16 | RS16A_YEAST 1-143  
17 | 40S ribosomal protein S17 | RS17A_YEAST 1-136  
18 | 40S ribosomal protein S18 | RS18A_YEAST 1-146  
19 | 40S ribosomal protein S19 | RS19A_YEAST 1-144  
1S | 18S ribosomal RNA |   
20 | 40S ribosomal protein S20 | RS20_YEAST 1-121  
21 | 40S ribosomal protein S21 | RS21A_YEAST 1-87  
22 | 40S ribosomal protein S22 | RS22A_YEAST 1-130  
23 | 40S ribosomal protein S23 | RS23A_YEAST 1-145  
24 | 40S ribosomal protein S24 | RS24A_YEAST 1-135  
25 | 40S ribosomal protein S25 | RS25A_YEAST 1-108  
26 | 40S ribosomal protein S26 | RS26A_YEAST 1-119  
27 | 40S ribosomal protein S27 | RS27_YEAST 1-82  
28 | 40S ribosomal protein S28 | RS28A_YEAST 1-67  
29 | 40S ribosomal protein S29 | RS29A_YEAST 1-56  
2S | 25S ribosomal RNA |   
30 | 40S ribosomal protein S30 | RS30A_YEAST 1-63  
31 | 40S ribosomal protein S31 | RS27A_YEAST 1-152  
5S | 5S ribosomal RNA |   
60 | 60S ribosomal protein L10 | RL10_YEAST 1-221  
61 | 60S ribosomal protein L11 | RL11A_YEAST 1-174  
62 | 60S ribosomal protein L12 | RL12A_YEAST 1-165  
63 | 60S ribosomal protein L13 | RL13A_YEAST 1-199  
64 | 60S ribosomal protein L14 | RL14A_YEAST 1-138  
65 | 60S ribosomal protein L15 | RL15A_YEAST 1-204  
66 | 60S ribosomal protein L16 | RL16A_YEAST 1-199  
67 | 60S ribosomal protein L17 | RL17A_YEAST 1-184  
68 | 60S ribosomal protein L18 | RL18A_YEAST 1-186  
69 | 60S ribosomal protein L19 | RL19A_YEAST 1-189  
70 | 60S ribosomal protein L20 | RL20A_YEAST 1-172  
71 | 60S ribosomal protein L21 | RL21A_YEAST 1-160  
72 | 60S ribosomal protein L22 | RL22A_YEAST 1-121  
73 | 60S ribosomal protein L23 | RL23A_YEAST 1-137  
74 | 60S ribosomal protein L24 | RL24A_YEAST 1-155  
75 | 60S ribosomal protein L25 | RL25_YEAST 1-142  
76 | 60S ribosomal protein L26 | RL26A_YEAST 1-127  
77 | 60S ribosomal protein L27 | RL27A_YEAST 1-136  
78 | 60S ribosomal protein L28 | RL28_YEAST 1-149  
79 | 60S ribosomal protein L29 | RL29_YEAST 1-59  
80 | 60S ribosomal protein L30 | RL30_YEAST 1-105  
81 | 60S ribosomal protein L31 | RL31A_YEAST 1-113  
82 | 60S ribosomal protein L32 | RL32_YEAST 1-130  
83 | 60S ribosomal protein L33 | RL33A_YEAST 1-107  
84 | 60S ribosomal protein L34 | RL34A_YEAST 1-121  
85 | 60S ribosomal protein L35 | RL35A_YEAST 1-120  
86 | 60S ribosomal protein L36 | RL36A_YEAST 1-100  
87 | 60S ribosomal protein L37 | RL37A_YEAST 1-88  
88 | 60S ribosomal protein L38 | RL38_YEAST 1-78  
89 | 60S ribosomal protein L39 | RL39_YEAST 1-51  
8S | 5.8S ribosomal RNA |   
90 | 60S ribosomal protein L40 | RL401_YEAST 1-128  
91 | 60S ribosomal protein L41 | RL41A_YEAST 1-25  
92 | 60S ribosomal protein L42 | RL44A_YEAST 1-106  
93 | 60S ribosomal protein L43 | RL43A_YEAST 1-92  
L1 | 60S ribosomal protein L1 | RL1A_YEAST 1-217  
L2 | 60S ribosomal protein L2 | RL2A_YEAST 1-254  
L3 | 60S ribosomal protein L3 | RL3_YEAST 1-387  
L4 | 60S ribosomal protein L4 | RL4A_YEAST 1-362  
L5 | 60S ribosomal protein L5 | RL5_YEAST 1-297  
L6 | 60S ribosomal protein L6 | RL6A_YEAST 1-176  
L7 | 60S ribosomal protein L7 | RL7A_YEAST 1-244  
L8 | 60S ribosomal protein L8 | RL8A_YEAST 1-256  
L9 | 60S ribosomal protein L9 | RL9A_YEAST 1-191  
MR | messenger RNA |   
P0 | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-312  
PT | P/E-site initiator transfer RNAfMet |   
RC | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 1-319  
S0 | 40S ribosomal protein S0 | RSSA1_YEAST 1-252  
S1 | 40S ribosomal protein S1 | RS3A1_YEAST 1-255  
S2 | 40S ribosomal protein S2 | RS2_YEAST 1-254  
S3 | 40S ribosomal protein S3 | RS3_YEAST 1-240  
S4 | 40S ribosomal protein S4 | RS4A_YEAST 1-261  
S5 | 40S ribosomal protein S5 | RS5_YEAST 1-225  
S6 | 40S ribosomal protein S6 | RS6A_YEAST 1-236  
S7 | 40S ribosomal protein S7 | RS7A_YEAST 1-190  
S8 | 40S ribosomal protein S8 | RS8A_YEAST 1-200  
S9 | 40S ribosomal protein S9 | RS9A_YEAST 1-197  
  

> select /L

Nothing selected  

> select /L*

36194 atoms, 36880 bonds, 2 pseudobonds, 4602 residues, 4 models selected  

> select /S*

33308 atoms, 33872 bonds, 2 pseudobonds, 4218 residues, 4 models selected  

> select /1-31

465091 atoms, 515513 bonds, 17375 pseudobonds, 25662 residues, 14 models
selected  

> set bgColor black

> select add /S*

498399 atoms, 549385 bonds, 17377 pseudobonds, 29880 residues, 14 models
selected  

> select subtract /2S

357483 atoms, 391662 bonds, 12006 pseudobonds, 23291 residues, 14 models
selected  

> select add RC

Expected an objects specifier or a keyword  

> select add /RC

362373 atoms, 396658 bonds, 12006 pseudobonds, 23927 residues, 14 models
selected  

> name frozen

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

> name frozen ssu

Missing or invalid "objects" argument: empty atom specifier  

> name frozen ssu sel

> select ssu

362373 atoms, 396658 bonds, 12006 pseudobonds, 23927 residues, 14 models
selected  

> color (#!59 & sel) #fffc79ff

> select ~sel & ##selected

469631 atoms, 495444 bonds, 7139 pseudobonds, 45690 residues, 14 models
selected  

> color (#!59 & sel) #73fdffff

> color (#!59 & sel) #76d6ffff

> show #!58 models

> show #!57 models

> hide #!58 models

> hide #!57 models

> show #!60 models

> hide #!60 models

> select subtract #59/PT:54

469608 atoms, 495417 bonds, 7136 pseudobonds, 45689 residues, 14 models
selected  

> select up

469631 atoms, 495444 bonds, 7136 pseudobonds, 45690 residues, 14 models
selected  

> select up

832004 atoms, 892102 bonds, 19145 pseudobonds, 69617 residues, 14 models
selected  

> select clear

> show #!58 models

> hide #!59 models

> select /S*

33308 atoms, 33872 bonds, 2 pseudobonds, 4218 residues, 4 models selected  

> select /1-31

465091 atoms, 515513 bonds, 17375 pseudobonds, 25662 residues, 14 models
selected  

> select /S*

33308 atoms, 33872 bonds, 2 pseudobonds, 4218 residues, 4 models selected  

> select add /1-31

498399 atoms, 549385 bonds, 17377 pseudobonds, 29880 residues, 14 models
selected  

> select subtract /2S

357483 atoms, 391662 bonds, 12006 pseudobonds, 23291 residues, 14 models
selected  

> select add /RC

362373 atoms, 396658 bonds, 12006 pseudobonds, 23927 residues, 14 models
selected  

> name frozen ssu sel

> color (#!58 & sel) #fffc79ff

> select ~sel & ##selected

469631 atoms, 495444 bonds, 7139 pseudobonds, 45690 residues, 14 models
selected  

> color (#!58 & sel) #76d6ffff

> select #58/ET:53

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #58/PT:44

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select up

3288 atoms, 3672 bonds, 154 residues, 1 model selected  

> color sel #ff9300ff

> color sel #ff2600ff

> color sel #ff7e79ff

> show #!61 models

> select #61/eEF2:370

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

> select up

65 atoms, 64 bonds, 9 residues, 1 model selected  

> select up

6569 atoms, 6695 bonds, 842 residues, 1 model selected  

> select ~sel & ##selected

200497 atoms, 215019 bonds, 5069 pseudobonds, 16761 residues, 4 models
selected  

> hide sel cartoons

> select ~sel & ##selected

6569 atoms, 6695 bonds, 842 residues, 1 model selected  

> select add #58

215705 atoms, 231414 bonds, 4513 pseudobonds, 17924 residues, 4 models
selected  

> show #!1 models

> color zone #1 near sel distance 4

> color zone #1 near sel distance 8

[Repeated 1 time(s)]

> color zone #1 near #61 distance 8

> color zone #1 near sel distance 8

> color zone #1 near sel distance 20

[Repeated 1 time(s)]

> select clear

> select #58/PT:20

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #58/ET:44

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select up

3288 atoms, 3672 bonds, 154 residues, 1 model selected  

> select up

209136 atoms, 224719 bonds, 17082 residues, 1 model selected  

> select down

3288 atoms, 3672 bonds, 154 residues, 1 model selected  

> color sel #ff2600ff

> color zone #1 near sel distance 20

Drag select of 17872 residues, 10 pseudobonds, 1
MultiPostProcessor_PPout_9.mrc  

> color zone #1 near sel distance 20

> select #1

2 models selected  

> select #58/ET:45

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

> select add #58/PT:23

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select up

3288 atoms, 3672 bonds, 154 residues, 1 model selected  

> select up

209136 atoms, 224719 bonds, 17082 residues, 1 model selected  

> select down

3288 atoms, 3672 bonds, 154 residues, 1 model selected  

> color sel #ff9300ff

> color sel orange red

Drag select of 17870 residues, 11 pseudobonds, 1
MultiPostProcessor_PPout_9.mrc  

> color zone #1 near sel distance 20

Drag select of 17924 residues, 11 pseudobonds, 1
MultiPostProcessor_PPout_9.mrc  

> select add #58

215705 atoms, 224719 bonds, 4513 pseudobonds, 17924 residues, 6 models
selected  

> select subtract #58

6569 atoms, 842 residues, 3 models selected  

> select add #58

215705 atoms, 224719 bonds, 4513 pseudobonds, 17924 residues, 6 models
selected  

> color zone #1 near sel distance 20

> hide #!58 models

> hide #!61 models

> color zone #1 near sel distance 18

[Repeated 1 time(s)]

> color zone #1 near sel distance 12

[Repeated 1 time(s)]

> set bgColor white

> volume splitbyzone #1

Opened MultiPostProcessor_PPout_9.mrc 0 as #2.1, grid size 128,128,128, pixel
4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_9.mrc 1 as #2.2, grid size 128,128,128, pixel
4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_9.mrc 2 as #2.3, grid size 128,128,128, pixel
4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_9.mrc 3 as #2.4, grid size 128,128,128, pixel
4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_9.mrc 4 as #2.5, grid size 128,128,128, pixel
4, shown at level 0.7, step 1, values float32  

> hide #!2.1 models

> save /Users/campbell/Desktop/Chimera_sessions/subunit_colouring.cxs
> includeMaps true

——— End of log from Wed Sep 11 21:36:06 2024 ———

opened ChimeraX session  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/62_tRNA_AP_T4_correctedmask/3/MultiPostProcessor_PPout_3.mrc

Opened MultiPostProcessor_PPout_3.mrc as #3, grid size 128,128,128, pixel 4,
shown at level 0.886, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/62_tRNA_AP_T4_correctedmask/6/MultiPostProcessor_PPout_6.mrc

Opened MultiPostProcessor_PPout_6.mrc as #4, grid size 128,128,128, pixel 4,
shown at level 0.923, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/62_tRNA_AP_T4_correctedmask/7/MultiPostProcessor_PPout_7.mrc

Opened MultiPostProcessor_PPout_7.mrc as #5, grid size 128,128,128, pixel 4,
shown at level 0.918, step 1, values float32  

> volume #3-5 level 0.6

> fitmap #3-5 inMap #50 eachModel true

Fit map MultiPostProcessor_PPout_3.mrc in map Stable_60S.mrc using 60646
points  
correlation = 0.7983, correlation about mean = 0.3571, overlap = 2.908e+04  
steps = 120, shift = 0.621, angle = 1.04 degrees  
  
Position of MultiPostProcessor_PPout_3.mrc (#3) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99990950 -0.00801887 -0.01080191 4.09340242  
0.00788770 0.99989530 -0.01213160 0.88692242  
0.01089807 0.01204530 0.99986806 -5.71180785  
Axis 0.66838290 -0.59990699 0.43974526  
Axis point 0.00000000 463.54507836 53.88459659  
Rotation angle (degrees) 1.03631485  
Shift along axis -0.30785120  
  
Fit map MultiPostProcessor_PPout_6.mrc in map Stable_60S.mrc using 59716
points  
correlation = 0.7946, correlation about mean = 0.3491, overlap = 2.996e+04  
steps = 64, shift = 0.659, angle = 0.882 degrees  
  
Position of MultiPostProcessor_PPout_6.mrc (#4) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99988156 0.01401975 0.00634933 -4.94155467  
-0.01401930 0.99990172 -0.00011535 3.06447694  
-0.00635033 0.00002632 0.99997984 1.08175760  
Axis 0.00460240 0.41257678 -0.91091120  
Axis point 208.56607079 354.31707192 0.00000000  
Rotation angle (degrees) 0.88185467  
Shift along axis 0.25620390  
  
Fit map MultiPostProcessor_PPout_7.mrc in map Stable_60S.mrc using 58821
points  
correlation = 0.7948, correlation about mean = 0.3368, overlap = 2.98e+04  
steps = 96, shift = 0.848, angle = 0.703 degrees  
  
Position of MultiPostProcessor_PPout_7.mrc (#5) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99995627 -0.00536984 0.00765621 -0.35623266  
0.00530892 0.99995426 0.00795550 -2.56661137  
-0.00769858 -0.00791450 0.99993904 3.43286921  
Axis -0.64699433 0.62599028 0.43535561  
Axis point 0.00000000 424.65998949 334.37315311  
Rotation angle (degrees) 0.70271639  
Shift along axis 0.11832559  
  

> hide #!2 models

> hide #!2.2 models

> show #!2.2 models

> hide #!2 models

> show #!2.1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!58 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!58 models

> show #!59 models

> select subtract #58

6569 atoms, 842 residues, 1 model selected  

> select add #59

214320 atoms, 223107 bonds, 4428 pseudobonds, 17906 residues, 4 models
selected  

> select clear

> select #59/2S:2253

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #59/PT:28

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select up

71944 atoms, 80521 bonds, 3364 residues, 1 model selected  

> show #!60 models

> hide #!59 models

> show #!61 models

> hide #!60 models

> select add #61

279010 atoms, 302235 bonds, 5069 pseudobonds, 20967 residues, 5 models
selected  

> show sel & #!61 cartoons

> show #!60 models

> hide #!61 models

> select add #60

487061 atoms, 524797 bonds, 10204 pseudobonds, 38835 residues, 9 models
selected  

> show sel & #!60 cartoons

> select #60/25S:2477

23 atoms, 25 bonds, 1 residue, 1 model selected  

> close #51-57

> close #2

> show #!50 models

> hide #!50 models

> show #!50 models

> open 5lzs

5lzs title:  
Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA,
eEF1A, and didemnin B [more info...]  
  
Chain information for 5lzs #2  
---  
Chain | Description | UniProt  
2 ii | tRNA |   
3 | E-site tRNA |   
5 | 28S ribosomal RNA |   
7 | 5S ribosomal RNA |   
8 | 5.8S ribosomal RNA |   
9 | 18S ribosomal RNA |   
A | uL2 | G1TT27_RABIT 1-257  
AA | uS2 |   
B | uL3 | G1TL06_RABIT 2-403  
BB | 40S ribosomal protein S3a | G1SS70_RABIT 1-264  
C | uL4 | G1SVW5_RABIT 1-378  
CC | uS5 |   
D | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297  
DD | uS4 | G1TNM3_RABIT 1-243  
E | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291  
EE | 40S ribosomal protein S4 |   
F | uL30 | G1TUB1_RABIT 1-247  
FF | Uncharacterized protein | G1TFM5_RABIT 1-204  
G | eL8 | G1STW0_RABIT 78-319  
GG | 40S ribosomal protein S6 | G1TM55_RABIT 1-249  
H | uL6 | G1TX33_RABIT 1-192  
HH | uS7 | G1SVB0_RABIT 1-194  
I | Ribosomal protein L10 (Predicted) | B7NZQ2_RABIT 1-214  
II | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208  
J | uL5 | G1TUB8_RABIT 1-178  
JJ | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194  
KK | eS10 | G1TPV3_RABIT 1-165  
L | eL13 |   
LL | uS17 | G1TRM4_RABIT 1-158  
M | eL14 | G1SZ12_RABIT 1-218  
MM | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132  
N | Ribosomal protein L15 | G1T0C1_RABIT 1-204  
NN | uS15 | G1SP51_RABIT 1-151  
O | uL13 |   
OO | uS11 | G1T1F0_RABIT -4-151  
P | uL22 | G1TVT6_RABIT 1-184  
PP | uS19 | G1U0Q2_RABIT 1-145  
Q | eL18 |   
QQ | uS9 | G1SGX4_RABIT 1-146  
R | eL19 |   
RR | eS17 | G1TU13_RABIT 1-135  
S | eL20 |   
SS | uS13 | G1TPG3_RABIT 1-152  
T | eL21 | G1SHQ2_RABIT 1-160  
TT | eS19 | G1TN62_RABIT 1-145  
U | eL22 |   
UU | uS10 | G1SIZ2_RABIT 1-119  
V | uL14 | G1T6D1_RABIT 1-140  
VV | eS21 |   
W | uL24 | G1SE28_RABIT 1-157  
WW | uS8 | G1TG89_RABIT 1-130  
X | uL23 | G1SE76_RABIT 1-156  
XX | uS12 |   
Y | uL24 | G1SQH0_RABIT 1-145  
YY | eS24 |   
Z | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136  
ZZ | eS25 | G1TDB3_RABIT 1-125  
a | uL15 | G1SNY0_RABIT 1-148  
aa | eS26 |   
b | eL29 | G1SGR6_RABIT 1-226  
bb | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84  
c | eL30 | G1TDL2_RABIT 1-115  
cc | eS28 | G1TIB4_RABIT 1-69  
d | eL31 | G1SHG0_RABIT 1-125  
dd | uS14 | G1U7M4_RABIT 1-56  
e | eL32 | G1U437_RABIT 1-135  
ee | eS30 | G1T8A2_RABIT 0-132  
f | eL33 | G1SF08_RABIT 1-110  
ff | eS31 | G1SK22_RABIT 1-156  
g | eL34 | G1U945_RABIT 1-116  
gg | RACK1 | G1SJB4_RABIT 1-317  
h | uL29 | G1SIT5_RABIT 1-123  
hh | mRNA |   
i | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105  
j | Ribosomal protein L37 | U3KPD5_RABIT 1-97  
jj | Elongation factor 1-alpha 1 | EF1A1_RABIT 1-462  
k | eL38 |   
l | eL39 | G1TTN1_RABIT 1-51  
m | eL40 |   
n | 60s ribosomal protein l41 |   
o | eL42 | G1U344_RABIT 1-106  
p | eL43 | G1SY53_RABIT 1-92  
r | eL28 | G1U7L1_RABIT 1-137  
s | uL10 |   
t | uL11 | G1SMR7_RABIT 1-165  
  
Non-standard residues in 5lzs #2  
---  
7C4 —
(2~{S})-~{N}-[(2~{R})-1-[[(3~{S},6~{S},8~{S},12~{S},13~{R},16~{S},17~{R},20~{S},23~{S})-13-[(2~{S})-butan-2-yl]-20-[(4-methoxyphenyl)methyl]-6,17,21-trimethyl-3-(2-methylpropyl)-12-oxidanyl-2,5,7,10,15,19,22-heptakis(oxidanylidene)-8-propan-2-yl-9,18-dioxa-1,4,14,21-tetrazabicyclo[21.3.0]hexacosan-16-yl]amino]-4-methyl-1-oxidanylidene-
pentan-2-yl]-~{N}-methyl-1-[(2~{S})-2-oxidanylpropanoyl]pyrrolidine-2-carboxamide  
GDP — guanosine-5'-diphosphate  
MG — magnesium ion  
ZN — zinc ion  
  

> hide #!60 models

> select #2/BB:230@CG

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,80.376,0,1,0,51.305,0,0,1,17.379

> hide sel atoms

> show sel cartoons

> select up

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

> select up

73 atoms, 73 bonds, 9 residues, 1 model selected  

> select up

1729 atoms, 1756 bonds, 213 residues, 1 model selected  

> select up

220934 atoms, 236952 bonds, 18186 residues, 1 model selected  

> select up

1052938 atoms, 1129054 bonds, 87803 residues, 15 models selected  

> select down

220934 atoms, 236952 bonds, 18186 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> view matrix models
> #2,0.41695,0.69159,0.58979,-137.31,-0.038035,0.66159,-0.7489,370.5,-0.90813,0.28982,0.30216,363.09

> view matrix models
> #2,0.41695,0.69159,0.58979,-169.89,-0.038035,0.66159,-0.7489,325.57,-0.90813,0.28982,0.30216,374.66

> view matrix models
> #2,-0.095311,-0.51285,-0.85317,718.77,-0.94128,0.32531,-0.090391,469.37,0.3239,0.79446,-0.51374,141.94

> view matrix models
> #2,-0.095311,-0.51285,-0.85317,845.1,-0.94128,0.32531,-0.090391,600.94,0.3239,0.79446,-0.51374,126.58

> view matrix models
> #2,-0.095311,-0.51285,-0.85317,816.92,-0.94128,0.32531,-0.090391,597.33,0.3239,0.79446,-0.51374,112.2

> view matrix models
> #2,-0.16685,-0.05941,-0.98419,740.32,-0.57495,-0.80504,0.14607,765.47,-0.80099,0.59023,0.10016,287.03

> view matrix models
> #2,-0.76725,-0.03844,-0.6402,791.22,-0.4463,-0.68487,0.57599,576.27,-0.46059,0.72765,0.50831,44.642

> view matrix models
> #2,-0.9867,-0.0032728,-0.16249,702.57,-0.14017,-0.48892,0.86099,360.38,-0.082264,0.87232,0.48196,-87.053

> view matrix models
> #2,-0.50714,-0.15757,0.84734,339.66,0.7856,0.31982,0.52967,-18.888,-0.35446,0.93428,-0.038411,111.49

> view matrix models
> #2,0.42444,0.60141,0.67687,-71.988,0.5063,0.46212,-0.72808,366.05,-0.75067,0.65173,-0.10835,315.03

> view matrix models
> #2,0.42444,0.60141,0.67687,-227.59,0.5063,0.46212,-0.72808,192.13,-0.75067,0.65173,-0.10835,320.5

> view matrix models
> #2,0.47291,0.76048,0.44501,-220.91,0.34661,0.30377,-0.88746,324.09,-0.81007,0.57393,-0.11993,361.63

> view matrix models
> #2,0.47291,0.76048,0.44501,-221.04,0.34661,0.30377,-0.88746,321.55,-0.81007,0.57393,-0.11993,366.79

> fitmap #2 inMap #50

Fit molecule 5lzs (#2) to map Stable_60S.mrc (#50) using 220934 atoms  
average map value = 0.5098, steps = 184  
shifted from previous position = 29.4  
rotated from previous position = 42.7 degrees  
atoms outside contour = 107640, contour level = 0.6  
  
Position of 5lzs (#2) relative to Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.16308926 0.97023782 -0.17899853 -30.30121573  
0.16359973 -0.20551056 -0.96488369 527.70842311  
-0.97295273 0.12807806 -0.19224721 533.87612945  
Axis 0.69464879 0.50460991 -0.51267134  
Axis point 0.00000000 93.04956583 445.54572911  
Rotation angle (degrees) 128.12172776  
Shift along axis -28.46479848  
  

> select clear

> log metadata #2

Metadata for 5lzs #2  
---  
Title | Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA, eEF1A, and didemnin B  
Citations | Shao, S., Murray, J., Brown, A., Taunton, J., Ramakrishnan, V., Hegde, R.S. (2016). Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes. Cell, 167, 1229-1240.e15. PMID: 27863242. DOI: 10.1016/j.cell.2016.10.046  
Shao, S., Murray, J., Brown, A., Taunton, J., Ramakrishnan, V., Hegde, R.S.
(?). Decoding mammalian ribosome-mRNA states by translational GTPase
complexes. To Be Published  
Non-standard residues | 7C4 — (2~{S})-~{N}-[(2~{R})-1-[[(3~{S},6~{S},8~{S},12~{S},13~{R},16~{S},17~{R},20~{S},23~{S})-13-[(2~{S})-butan-2-yl]-20-[(4-methoxyphenyl)methyl]-6,17,21-trimethyl-3-(2-methylpropyl)-12-oxidanyl-2,5,7,10,15,19,22-heptakis(oxidanylidene)-8-propan-2-yl-9,18-dioxa-1,4,14,21-tetrazabicyclo[21.3.0]hexacosan-16-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-~{N}-methyl-1-[(2~{S})-2-oxidanylpropanoyl]pyrrolidine-2-carboxamide  
GDP — guanosine-5'-diphosphate  
MG — magnesium ion  
ZN — zinc ion  
Source (natural) | Oryctolagus cuniculus (rabbit)  
CryoEM Map | EMDB 4130 — open map  
Experimental method | Electron microscopy  
Resolution | 3.31Å  
  
> log chains #2

Chain information for 5lzs #2  
---  
Chain | Description | UniProt  
2 ii | tRNA |   
3 | E-site tRNA |   
5 | 28S ribosomal RNA |   
7 | 5S ribosomal RNA |   
8 | 5.8S ribosomal RNA |   
9 | 18S ribosomal RNA |   
A | uL2 | G1TT27_RABIT 1-257  
AA | uS2 |   
B | uL3 | G1TL06_RABIT 2-403  
BB | 40S ribosomal protein S3a | G1SS70_RABIT 1-264  
C | uL4 | G1SVW5_RABIT 1-378  
CC | uS5 |   
D | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297  
DD | uS4 | G1TNM3_RABIT 1-243  
E | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291  
EE | 40S ribosomal protein S4 |   
F | uL30 | G1TUB1_RABIT 1-247  
FF | Uncharacterized protein | G1TFM5_RABIT 1-204  
G | eL8 | G1STW0_RABIT 78-319  
GG | 40S ribosomal protein S6 | G1TM55_RABIT 1-249  
H | uL6 | G1TX33_RABIT 1-192  
HH | uS7 | G1SVB0_RABIT 1-194  
I | Ribosomal protein L10 (Predicted) | B7NZQ2_RABIT 1-214  
II | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208  
J | uL5 | G1TUB8_RABIT 1-178  
JJ | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194  
KK | eS10 | G1TPV3_RABIT 1-165  
L | eL13 |   
LL | uS17 | G1TRM4_RABIT 1-158  
M | eL14 | G1SZ12_RABIT 1-218  
MM | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132  
N | Ribosomal protein L15 | G1T0C1_RABIT 1-204  
NN | uS15 | G1SP51_RABIT 1-151  
O | uL13 |   
OO | uS11 | G1T1F0_RABIT -4-151  
P | uL22 | G1TVT6_RABIT 1-184  
PP | uS19 | G1U0Q2_RABIT 1-145  
Q | eL18 |   
QQ | uS9 | G1SGX4_RABIT 1-146  
R | eL19 |   
RR | eS17 | G1TU13_RABIT 1-135  
S | eL20 |   
SS | uS13 | G1TPG3_RABIT 1-152  
T | eL21 | G1SHQ2_RABIT 1-160  
TT | eS19 | G1TN62_RABIT 1-145  
U | eL22 |   
UU | uS10 | G1SIZ2_RABIT 1-119  
V | uL14 | G1T6D1_RABIT 1-140  
VV | eS21 |   
W | uL24 | G1SE28_RABIT 1-157  
WW | uS8 | G1TG89_RABIT 1-130  
X | uL23 | G1SE76_RABIT 1-156  
XX | uS12 |   
Y | uL24 | G1SQH0_RABIT 1-145  
YY | eS24 |   
Z | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136  
ZZ | eS25 | G1TDB3_RABIT 1-125  
a | uL15 | G1SNY0_RABIT 1-148  
aa | eS26 |   
b | eL29 | G1SGR6_RABIT 1-226  
bb | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84  
c | eL30 | G1TDL2_RABIT 1-115  
cc | eS28 | G1TIB4_RABIT 1-69  
d | eL31 | G1SHG0_RABIT 1-125  
dd | uS14 | G1U7M4_RABIT 1-56  
e | eL32 | G1U437_RABIT 1-135  
ee | eS30 | G1T8A2_RABIT 0-132  
f | eL33 | G1SF08_RABIT 1-110  
ff | eS31 | G1SK22_RABIT 1-156  
g | eL34 | G1U945_RABIT 1-116  
gg | RACK1 | G1SJB4_RABIT 1-317  
h | uL29 | G1SIT5_RABIT 1-123  
hh | mRNA |   
i | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105  
j | Ribosomal protein L37 | U3KPD5_RABIT 1-97  
jj | Elongation factor 1-alpha 1 | EF1A1_RABIT 1-462  
k | eL38 |   
l | eL39 | G1TTN1_RABIT 1-51  
m | eL40 |   
n | 60s ribosomal protein l41 |   
o | eL42 | G1U344_RABIT 1-106  
p | eL43 | G1SY53_RABIT 1-92  
r | eL28 | G1U7L1_RABIT 1-137  
s | uL10 |   
t | uL11 | G1SMR7_RABIT 1-165  
  

> hide #!50 models

> show #!50 models

> hide #!50 models

Drag select of 7177 residues, 4 pseudobonds  

> select up

123617 atoms, 134235 bonds, 4 pseudobonds, 8832 residues, 2 models selected  

> select up

130885 atoms, 141645 bonds, 4 pseudobonds, 9737 residues, 2 models selected  

> select #2/W:107

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

> undo

> select add #2/W:104

130894 atoms, 141653 bonds, 4 pseudobonds, 9738 residues, 2 models selected  

> select add #2/p:85

130905 atoms, 141663 bonds, 4 pseudobonds, 9739 residues, 2 models selected  

> select up

131257 atoms, 142014 bonds, 4 pseudobonds, 9785 residues, 2 models selected  

> select up

131986 atoms, 142756 bonds, 4 pseudobonds, 9880 residues, 2 models selected  

> select up

132017 atoms, 142786 bonds, 4 pseudobonds, 9884 residues, 2 models selected  

> select up

132514 atoms, 143297 bonds, 4 pseudobonds, 9943 residues, 2 models selected  

> select up

132723 atoms, 143297 bonds, 4 pseudobonds, 10152 residues, 2 models selected  

> select up

220934 atoms, 236952 bonds, 22 pseudobonds, 18186 residues, 2 models selected  

> select down

132723 atoms, 143297 bonds, 4 pseudobonds, 10152 residues, 2 models selected  

> select add #2/c:37

132731 atoms, 143304 bonds, 4 pseudobonds, 10153 residues, 2 models selected  

> select add #2/A:139

132741 atoms, 143314 bonds, 4 pseudobonds, 10154 residues, 2 models selected  

> select up

132871 atoms, 143445 bonds, 4 pseudobonds, 10171 residues, 2 models selected  

> select up

135382 atoms, 146004 bonds, 4 pseudobonds, 10498 residues, 2 models selected  

> select add #2/Z:113

135391 atoms, 146012 bonds, 4 pseudobonds, 10499 residues, 2 models selected  

> select up

135577 atoms, 146201 bonds, 4 pseudobonds, 10521 residues, 2 models selected  

> select up

136489 atoms, 147134 bonds, 4 pseudobonds, 10633 residues, 2 models selected  

> select down

135577 atoms, 146201 bonds, 4 pseudobonds, 10521 residues, 2 models selected  

> select up

136489 atoms, 147134 bonds, 4 pseudobonds, 10633 residues, 2 models selected  

> select ~sel & ##selected

84445 atoms, 89818 bonds, 1855 pseudobonds, 7553 residues, 4 models selected  

> select subtract /t

83285 atoms, 88644 bonds, 1855 pseudobonds, 7400 residues, 4 models selected  

> select subtract /V

82250 atoms, 87596 bonds, 1854 pseudobonds, 7260 residues, 4 models selected  

> color (#!2 & sel) #fffc79ff

> select ~sel & ##selected

138684 atoms, 149356 bonds, 4033 pseudobonds, 10926 residues, 4 models
selected  

> color (#!2 & sel) #76d6ffff

> select #2/jj:179

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

> select up

172 atoms, 173 bonds, 20 residues, 1 model selected  

> select up

3383 atoms, 3453 bonds, 441 residues, 1 model selected  

> select up

3491 atoms, 3565 bonds, 444 residues, 1 model selected  

> color sel forest green

> select #2/ii:45

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

> select add #2/2:51

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #2/3:53

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select up

4825 atoms, 5391 bonds, 227 residues, 1 model selected  

> select up

220934 atoms, 236952 bonds, 18186 residues, 1 model selected  

> select down

4825 atoms, 5391 bonds, 227 residues, 1 model selected  

> color sel orange red

> show #!4 models

> ui tool show "Color Zone"

> color zone #4 near #2 distance 8

> show #!58 models

> select #58/2S:2470

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

> select #58/2S:2467

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #58/2S:2479

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

> select add #58/L1:70

28 atoms, 28 bonds, 2 residues, 1 model selected  

> select up

71578 atoms, 80017 bonds, 3424 residues, 1 model selected  

> select up

72225 atoms, 80672 bonds, 3506 residues, 1 model selected  

> color zone #4 near sel distance 8

> select 5lzs

Expected an objects specifier or a keyword  

> select #2

220934 atoms, 236952 bonds, 5887 pseudobonds, 18186 residues, 4 models
selected  

> select add #2

293159 atoms, 317624 bonds, 5887 pseudobonds, 21692 residues, 5 models
selected  

> select subtract #2/3

291566 atoms, 315845 bonds, 5821 pseudobonds, 21617 residues, 5 models
selected  

> color zone #4 near sel distance 8

[Repeated 1 time(s)]

> select add #58/ET:53

291589 atoms, 315870 bonds, 5821 pseudobonds, 21618 residues, 7 models
selected  

> select up

293210 atoms, 317681 bonds, 5821 pseudobonds, 21694 residues, 7 models
selected  

> select up

430070 atoms, 461671 bonds, 5887 pseudobonds, 35268 residues, 7 models
selected  

> color zone #4 near sel distance 8

> lighting flat

> lighting simple

> lighting full

> select #2/3:26

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

> select add #58/ET:28

42 atoms, 45 bonds, 2 residues, 2 models selected  

> select up

3237 atoms, 3615 bonds, 152 residues, 2 models selected  

> select up

430070 atoms, 461671 bonds, 35268 residues, 2 models selected  

> select up

1052938 atoms, 1129054 bonds, 87803 residues, 15 models selected  

> select down

430070 atoms, 461671 bonds, 35268 residues, 2 models selected  

> select down

3237 atoms, 3615 bonds, 152 residues, 2 models selected  

> color sel #73fdffff

> color sel #76d6ffff

> select up

430070 atoms, 461671 bonds, 35268 residues, 2 models selected  

> select up

1052938 atoms, 1129054 bonds, 87803 residues, 15 models selected  

> select up

1052938 atoms, 1129054 bonds, 87803 residues, 15 models selected  

> color zone #4 near sel distance 8

> select down

430070 atoms, 461671 bonds, 35268 residues, 2 models selected  

> color zone #4 near sel distance 8

> hide #!4 models

> show #!4 models

> hide #!58 models

> hide #!2 models

> lighting soft

> save /Users/campbell/Desktop/image2.png supersample 3

> hide #!4 models

> show #!5 models

> open 6tnu

6tnu title:  
Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs.
[more info...]  
  
Chain information for 6tnu #6  
---  
Chain | Description | UniProt  
2 | 18S rRNA |   
A | 40S ribosomal protein S3 | RS3_YEAST 4-225  
AA | 60S ribosomal protein L8-A | RL8A_YEAST 24-256  
AB | 60S ribosomal protein L23-A | RL23A_YEAST 2-137  
AC | 60S ribosomal protein L36-A | RL36A_YEAST 2-100  
AD | 60S ribosomal protein L9-A | RL9A_YEAST 1-191  
AE | 60S ribosomal protein L24-A | RL24A_YEAST 1-126  
AF | 60S ribosomal protein L37-A | RL37A_YEAST 2-82  
AG | 60S ribosomal protein L11-B | RL11B_YEAST 6-174  
AH | 60S ribosomal protein L25 | RL25_YEAST 22-142  
AI | 60S ribosomal protein L38 | RL38_YEAST 2-78  
AJ | 60S ribosomal protein L13-A | RL13A_YEAST 2-194  
AK | 60S ribosomal protein L26-A | RL26A_YEAST 2-126  
AL | 60S ribosomal protein L39 | RL39_YEAST 2-51  
AM | 60S ribosomal protein L14-A | RL14A_YEAST 3-138  
AN | 60S ribosomal protein L27-A | RL27A_YEAST 2-136  
AO | Ubiquitin-60S ribosomal protein L40 | RL40A_YEAST 77-128  
AP | 60S ribosomal protein L42-A | RL44A_YEAST 2-104  
AQ | 60S ribosomal protein L15-A | RL15A_YEAST 2-204  
AR | 60S ribosomal protein L28 | RL28_YEAST 2-149  
AS | 60S ribosomal protein L41-A |   
AT | 60S ribosomal protein L43-A | RL43A_YEAST 2-92  
AU | 60S ribosomal protein L16-A | RL16A_YEAST 3-199  
AV | 60S ribosomal protein L29 | RL29_YEAST 2-59  
AW | 60S ribosomal protein L2-A | RL2A_YEAST 2-252  
AX | 60S ribosomal protein L17-A | RL17A_YEAST 2-184  
AY | 60S ribosomal protein L30 | RL30_YEAST 9-104  
B | Rps5p | A0A1L4AA68_YEASX 20-225  
BA | 60S ribosomal protein L3 | RL3_YEAST 2-387  
BB | 60S ribosomal protein L18-A | RL18A_YEAST 2-186  
BC | 60S ribosomal protein L31-A | RL31A_YEAST 4-112  
BD | 60S ribosomal protein L10 | RL10_YEAST 2-219  
BE | 60S ribosomal protein L4-A | RL4A_YEAST 2-362  
BF | 60S ribosomal protein L19-A | RL19A_YEAST 2-189  
BG | 60S ribosomal protein L32 | RL32_YEAST 2-128  
BH | 60S ribosomal protein L20-A | RL20A_YEAST 2-172  
BI | 60S ribosomal protein L5 | RL5_YEAST 4-297  
BJ | 60S ribosomal protein L21-A | RL21A_YEAST 2-160  
BK | 60S ribosomal protein L33-A | RL33A_YEAST 2-107  
BL | 60S ribosomal protein L22-A | RL22A_YEAST 9-108  
BM | 60S ribosomal protein L6-B | RL6B_YEAST 2-176  
BN | 60S ribosomal protein L34-A | RL34A_YEAST 2-113  
BO | 60S ribosomal protein L7-A | RL7A_YEAST 23-244  
BP | 60S ribosomal protein L35-A | RL35A_YEAST 2-120  
BQ | 25S rRNA |   
BR | 5S rRNA |   
BS | 5.8S rRNA |   
BT | 60S ribosomal protein L1 |   
C | 40S ribosomal protein S10-A | RS10A_YEAST 1-92  
D | 40S ribosomal protein S12 | RS12_YEAST 23-143  
E | 40S ribosomal protein S15 | RS15_YEAST 13-129  
F | 40S ribosomal protein S16-A | RS16A_YEAST 3-143  
G | 40S ribosomal protein S17-B | RS17B_YEAST 2-126  
H | 40S ribosomal protein S18-A | RS18A_YEAST 2-146  
I | 40S ribosomal protein S19-A | RS19A_YEAST 2-144  
J | 40S ribosomal protein S20 | RS20_YEAST 20-119  
K | 40S ribosomal protein S25-A | RS25A_YEAST 24-105  
L | 40S ribosomal protein S28-A | RS28A_YEAST 5-67  
M | 40S ribosomal protein S29-A | RS29A_YEAST 4-56  
N | Ubiquitin-40S ribosomal protein S31 | RS31_YEAST 80-152  
O | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 5-316  
P | 40S ribosomal protein S0-A | RSSA1_YEAS1 2-207  
Q | 40S ribosomal protein S1-A | RS3A1_YEAS1 2-233  
R | 40S ribosomal protein S2 | RS2_YEAST 34-249  
S | 40S ribosomal protein S4-A | RS4A_YEAST 2-259  
T | 40S ribosomal protein S6-A | RS6A_YEAST 1-228  
U | 40S ribosomal protein S7-A | RS7A_YEAST 4-187  
V | 40S ribosomal protein S8 | A0A0J9X221_LACKL 2-199  
W | 40S ribosomal protein S9-A | RS9A_YEAST 2-185  
X | 40S ribosomal protein S11-A | RS11A_YEAST 4-145  
Y | 40S ribosomal protein S13 | RS13_YEAST 2-151  
Z | 40S ribosomal protein S14-B | RS14B_YEAST 11-137  
a | 40S ribosomal protein S21-A | RS21A_YEAST 1-87  
b | 40S ribosomal protein S22-A | RS22A_YEAST 2-130  
c | 40S ribosomal protein S23-A | RS23A_YEAST 2-145  
d | 40S ribosomal protein S24-A | RS24A_YEAST 2-135  
e | 40S ribosomal protein S26-B | RS26B_YEAST 2-98  
eI | Eukaryotic translation initiation factor 5A-1 | IF5A1_YEAST 4-157  
f | 40S ribosomal protein S27-A | RS27A_YEAST 2-82  
g | 40S ribosomal protein S30-A | RS30A_YEAST 2-61  
l | mRNA |   
m | A-site tRNA |   
n | P-site tRNA |   
  
Non-standard residues in 6tnu #6  
---  
3HE —
4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
ZN — zinc ion  
  
1555 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select #6/2:821@C4'

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

37739 atoms, 42211 bonds, 1771 residues, 1 model selected  

> select up

204962 atoms, 220182 bonds, 16898 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> view matrix models #6,1,0,0,96.908,0,1,0,55.063,0,0,1,13.276

> view matrix models #6,1,0,0,188.67,0,1,0,110.82,0,0,1,20.101

> view matrix models
> #6,0.51919,0.85456,0.013246,71.949,-0.22449,0.15131,-0.96266,639.52,-0.82465,0.49683,0.2704,272.76

> view matrix models
> #6,-0.15462,0.7946,-0.58711,406.1,-0.59319,-0.54989,-0.58801,826.94,-0.79008,0.25735,0.55637,257.28

> view matrix models
> #6,-0.10716,0.72846,-0.67666,434.9,-0.52992,-0.61769,-0.58106,827.97,-0.84125,0.29631,0.45222,285.58

> view matrix models
> #6,-0.10716,0.72846,-0.67666,433.12,-0.52992,-0.61769,-0.58106,829.22,-0.84125,0.29631,0.45222,281.74

> view matrix models
> #6,0.48051,0.87401,-0.072223,95.974,-0.23222,0.047385,-0.97151,673.16,-0.84569,0.48359,0.22573,288.98

> view matrix models
> #6,0.48051,0.87401,-0.072223,-87.741,-0.23222,0.047385,-0.97151,551.63,-0.84569,0.48359,0.22573,291.04

> fitmap #2 inMap #5

Fit molecule 5lzs (#2) to map MultiPostProcessor_PPout_7.mrc (#5) using 220934
atoms  
average map value = 0.773, steps = 48  
shifted from previous position = 0.922  
rotated from previous position = 1.34 degrees  
atoms outside contour = 49177, contour level = 0.6  
  
Position of 5lzs (#2) relative to MultiPostProcessor_PPout_7.mrc (#5)
coordinates:  
Matrix rotation and translation  
0.16730225 0.97268696 -0.16090383 -37.15841963  
0.16821694 -0.18897363 -0.96746681 522.61039443  
-0.97144893 0.13479262 -0.19523814 532.86139906  
Axis 0.69447790 0.51068346 -0.50685585  
Axis point 0.00000000 90.90558667 443.77382906  
Rotation angle (degrees) 127.47785571  
Shift along axis -29.00113860  
  

> fitmap #2 inMap #5

Fit molecule 5lzs (#2) to map MultiPostProcessor_PPout_7.mrc (#5) using 220934
atoms  
average map value = 0.773, steps = 44  
shifted from previous position = 0.0264  
rotated from previous position = 0.0106 degrees  
atoms outside contour = 49182, contour level = 0.6  
  
Position of 5lzs (#2) relative to MultiPostProcessor_PPout_7.mrc (#5)
coordinates:  
Matrix rotation and translation  
0.16720525 0.97271106 -0.16085897 -37.15793738  
0.16808242 -0.18889097 -0.96750633 522.62555614  
-0.97148891 0.13473457 -0.19507919 532.82119064  
Axis 0.69441772 0.51070124 -0.50692038  
Axis point 0.00000000 90.89150714 443.79401437  
Rotation angle (degrees) 127.47263581  
Shift along axis -28.99553276  
  

> fitmap #6 inMap #5

Fit molecule 6tnu (#6) to map MultiPostProcessor_PPout_7.mrc (#5) using 204962
atoms  
average map value = 0.8637, steps = 104  
shifted from previous position = 6.22  
rotated from previous position = 21.8 degrees  
atoms outside contour = 21197, contour level = 0.6  
  
Position of 6tnu (#6) relative to MultiPostProcessor_PPout_7.mrc (#5)
coordinates:  
Matrix rotation and translation  
0.15782578 0.98738484 0.01273570 -57.14848132  
-0.11290191 0.03085625 -0.99312691 524.36425700  
-0.98099143 0.15530314 0.11634755 443.24394993  
Axis 0.61237488 0.52988297 -0.58670354  
Axis point 0.00000000 40.79771785 497.35638831  
Rotation angle (degrees) 110.33357622  
Shift along axis -17.19739507  
  

> hide #!5 models

Drag select of 6883 residues, 1 pseudobonds  

> select up

114902 atoms, 124769 bonds, 1 pseudobond, 8350 residues, 2 models selected  

> select up

120557 atoms, 130539 bonds, 1 pseudobond, 9057 residues, 2 models selected  

> select #6/BT:143

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

> select add #6/BT:143

120562 atoms, 130543 bonds, 1 pseudobond, 9058 residues, 2 models selected  

> select up

120617 atoms, 130598 bonds, 1 pseudobond, 9069 residues, 2 models selected  

> select up

121607 atoms, 131588 bonds, 1 pseudobond, 9267 residues, 2 models selected  

> select add #6/AE:92

121612 atoms, 131592 bonds, 1 pseudobond, 9268 residues, 2 models selected  

> select up

121667 atoms, 131647 bonds, 1 pseudobond, 9279 residues, 2 models selected  

> select up

122443 atoms, 132438 bonds, 1 pseudobond, 9393 residues, 2 models selected  

> select add #6/AB:127

122450 atoms, 132445 bonds, 1 pseudobond, 9394 residues, 2 models selected  

> select up

122501 atoms, 132498 bonds, 1 pseudobond, 9400 residues, 2 models selected  

> select up

123446 atoms, 133456 bonds, 1 pseudobond, 9529 residues, 2 models selected  

> select ~sel & ##selected

81516 atoms, 86726 bonds, 1725 pseudobonds, 7369 residues, 4 models selected  

> select subtract /AN

80436 atoms, 85620 bonds, 1725 pseudobonds, 7234 residues, 4 models selected  

> select subtract /AY'

80436 atoms, 85620 bonds, 1725 pseudobonds, 7234 residues, 4 models selected  

> select subtract /AY

79699 atoms, 84875 bonds, 1725 pseudobonds, 7138 residues, 4 models selected  

> select subtract /AT

79004 atoms, 84174 bonds, 1721 pseudobonds, 7046 residues, 4 models selected  

> select subtract /AW

77105 atoms, 82241 bonds, 1721 pseudobonds, 6795 residues, 4 models selected  

> select subtract /el

77105 atoms, 82241 bonds, 1721 pseudobonds, 6795 residues, 4 models selected  

> select subtract /eI

75962 atoms, 81083 bonds, 1721 pseudobonds, 6641 residues, 4 models selected  

> color (#!6 & sel) #fffc79ff

> select ~sel & ##selected

129000 atoms, 139099 bonds, 3509 pseudobonds, 10257 residues, 4 models
selected  

> color (#!6 & sel) #76d6ffff

> select #6/m:45

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/n:46

47 atoms, 51 bonds, 2 residues, 1 model selected  

> select up

3235 atoms, 3613 bonds, 151 residues, 1 model selected  

> select up

204962 atoms, 220182 bonds, 16898 residues, 1 model selected  

> select down

3235 atoms, 3613 bonds, 151 residues, 1 model selected  

> color sel orange red

> select #6/eI:139

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

> select up

57 atoms, 56 bonds, 8 residues, 1 model selected  

> select up

1143 atoms, 1158 bonds, 154 residues, 1 model selected  

> color sel forest green

> show #!5 models

> select add #6

204962 atoms, 220182 bonds, 5230 pseudobonds, 16898 residues, 4 models
selected  

> color zone #5 near sel distance 24

> hide #!6 models

> lighting soft

> save /Users/campbell/Desktop/image3.png supersample 3

> show #!3 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!59 models

> show #!6 models

> hide #!6 models

> show #!6 models

> select subtract #6

Nothing selected  

> select add #59

207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models
selected  

> hide #!59 models

> hide #!6 models

> select subtract #59

Nothing selected  

> select subtract /eIopen 6gz7

Expected a keyword  

> open 6gz7

Summary of feedback from opening 6gz7 fetched from pdb  
---  
note | Fetching compressed mmCIF 6gz7 from http://files.rcsb.org/download/6gz7.cif  
  
6gz7 title:  
Polyamide - DNA complex NMR structure [more info...]  
  
Chain information for 6gz7  
---  
Chain | Description  
7.1/A 7.2/A 7.3/A 7.4/A 7.5/A 7.6/A 7.7/A 7.8/A 7.9/A 7.10/A 7.11/A 7.1/B 7.2/B 7.3/B 7.4/B 7.5/B 7.6/B 7.7/B 7.8/B 7.9/B 7.10/B 7.11/B | DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')  
  

> open 6gz5

6gz5 title:  
tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP
hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3) [more info...]  
  
Chain information for 6gz5 #8  
---  
Chain | Description  
A2 | 28S ribosomal RNA  
A3 | 5.8S ribosomal RNA  
A4 | 5S ribosomal RNA  
AA | ribosomal protein uL2  
AB | ribosomal protein uL3  
AC | ribosomal protein uL4  
AD | ribosomal protein uL18  
AE | ribosomal protein eL6  
AF | ribosomal protein uL30  
AG | ribosomal protein eL8  
AH | ribosomal protein uL6  
AI | ribosomal protein uL16  
AJ | ribosomal protein uL5  
AK | ribosomal protein uL10  
AL | ribosomal protein eL13  
AM | ribosomal protein eL14  
AN | ribosomal protein eL15  
AO | ribosomal protein uL13  
AP | ribosomal protein uL22  
AQ | ribosomal protein eL18  
AR | ribosomal protein eL19  
AS | ribosomal protein eL20  
AT | ribosomal protein eL21  
AU | ribosomal protein eL22  
AV | ribosomal protein uL14  
AW | ribosomal protein eL24  
AX | ribosomal protein uL23  
AY | ribosomal protein uL24  
AZ | ribosomal protein eL27  
Aa | ribosomal protein uL15  
Ab | ribosomal protein eL29  
Ac | ribosomal protein eL30  
Ad | ribosomal protein eL31  
Ae | ribosomal protein eL32  
Af | ribosomal protein eL33  
Ag | ribosomal protein eL34  
Ah | ribosomal protein uL29  
Ai | ribosomal protein eL36  
Aj | ribosomal protein eL37  
Ak | ribosomal protein eL38  
Al | ribosomal protein eL39  
Am | ribosomal protein eL40  
An | ribosomal protein eL41  
Ao | ribosomal protein eL42  
Ap | ribosomal protein eL43  
Aq | ribosomal protein uL11  
At | ribosomal protein eL28  
Au | ribosomal protein uL1  
B1 | 18S ribosomal RNA  
BA | ribosomal protein uS2  
BB | ribosomal protein eS1  
BC | ribosomal protein uS5  
BD | ribosomal protein uS3  
BE | ribosomal protein eS4  
BF | ribosomal protein uS7  
BG | ribosomal protein eS6  
BH | ribosomal protein eS7  
BI | ribosomal protein eS8  
BJ | ribosomal protein uS4  
BK | ribosomal protein eS10  
BL | ribosomal protein uS17  
BM | ribosomal protein eS12  
BN | ribosomal protein uS15  
BO | ribosomal protein uS11  
BP | ribosomal protein uS19  
BQ | ribosomal protein uS9  
BR | ribosomal protein eS17  
BS | ribosomal protein uS13  
BT | ribosomal protein eS19  
BU | ribosomal protein uS10  
BV | ribosomal protein eS21  
BW | ribosomal protein uS8  
BX | ribosomal protein uS12  
BY | ribosomal protein eS24  
BZ | ribosomal protein eS25  
Ba | ribosomal protein eS26  
Bb | ribosomal protein eS27  
Bc | ribosomal protein eS28  
Bd | ribosomal protein uS14  
Be | ribosomal protein eS30  
Bf | ribosomal protein eS31  
Bg | ribosomal protein RACK 1  
Bv | P/P-site-tRNA  
Bw | E/E-site-tRNA  
Bx | mRNA  
Ct | eukaryotic elongation factor 2 (eEF2)  
  
Non-standard residues in 6gz5 #8  
---  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
ZN — zinc ion  
  

> close #7

> select #8/A2:632@OP2

1 atom, 1 residue, 1 model selected  

> select up

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

77427 atoms, 86624 bonds, 3612 residues, 1 model selected  

> select up

77656 atoms, 86624 bonds, 3841 residues, 1 model selected  

> select up

225601 atoms, 241695 bonds, 18791 residues, 1 model selected  

> select up

1483501 atoms, 1590931 bonds, 123492 residues, 17 models selected  

> select down

225601 atoms, 241695 bonds, 18791 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> view matrix models #8,1,0,0,280.59,0,1,0,95.347,0,0,1,-14.904

> view matrix models
> #8,0.53386,0.26704,-0.8023,500,-0.49741,0.86647,-0.042577,236.26,0.6838,0.4218,0.5954,-155.56

> view matrix models
> #8,-0.18352,0.56975,-0.80107,603.04,-0.79091,-0.56951,-0.22386,590.77,-0.58376,0.59249,0.55514,99.427

> view matrix models
> #8,-0.66949,0.17477,-0.72197,762.57,0.72769,0.34947,-0.5902,172.28,0.14916,-0.9205,-0.36115,394.23

> view matrix models
> #8,0.27793,-0.010744,-0.96054,637.35,0.95554,0.10558,0.2753,-12.136,0.098458,-0.99435,0.039611,336.06

> view matrix models
> #8,0.80383,-0.26024,-0.53492,479.12,0.57053,0.082729,0.8171,-35.238,-0.16838,-0.96199,0.21497,352.64

> view matrix models
> #8,0.79149,0.53728,-0.29133,291.19,0.17954,0.25124,0.95113,-7.0749,0.58421,-0.80512,0.10239,183.72

> view matrix models
> #8,0.74092,0.0076392,0.67155,197.98,-0.64559,-0.26743,0.71533,312.98,0.18506,-0.96355,-0.19321,359.51

> view matrix models
> #8,0.74092,0.0076392,0.67155,1.8972,-0.64559,-0.26743,0.71533,224.34,0.18506,-0.96355,-0.19321,412.72

> view matrix models
> #8,0.74092,0.0076392,0.67155,-81.594,-0.64559,-0.26743,0.71533,282.81,0.18506,-0.96355,-0.19321,447.85

> view matrix models
> #8,0.79644,0.0032519,0.60471,-79.225,-0.5665,-0.34585,0.74797,272.66,0.21157,-0.93828,-0.27361,454.1

> view matrix models
> #8,0.83971,-0.076871,0.53757,-60.765,-0.53734,-0.26064,0.80208,240.16,0.078455,-0.96237,-0.26017,484.67

> view matrix models
> #8,0.83971,-0.076871,0.53757,-23.422,-0.53734,-0.26064,0.80208,243.29,0.078455,-0.96237,-0.26017,477.88

> fitmap #8 inMap #3

Fit molecule 6gz5 (#8) to map MultiPostProcessor_PPout_3.mrc (#3) using 225601
atoms  
average map value = 0.7158, steps = 148  
shifted from previous position = 12.3  
rotated from previous position = 31.1 degrees  
atoms outside contour = 62684, contour level = 0.6  
  
Position of 6gz5 (#8) relative to MultiPostProcessor_PPout_3.mrc (#3)
coordinates:  
Matrix rotation and translation  
0.98555011 -0.16435080 0.04098486 68.71830221  
-0.08024433 -0.23993378 0.96746711 118.30036800  
-0.14917034 -0.95677613 -0.24965498 510.53826995  
Axis -0.99421263 0.09824886 0.04345590  
Axis point 0.00000000 261.58202709 209.46786979  
Rotation angle (degrees) 104.59703757  
Shift along axis -34.51182807  
  

> hide #!3 models

> view matrix models
> #8,0.98772,-0.15208,0.03592,11.989,-0.070653,-0.2296,0.97072,98.487,-0.13938,-0.96133,-0.23752,506.41

Drag select of 7893 residues  

> select up

130107 atoms, 141177 bonds, 9391 residues, 1 model selected  

> select up

144988 atoms, 156335 bonds, 11284 residues, 1 model selected  

> select add #8/AZ:117

144997 atoms, 156343 bonds, 11285 residues, 1 model selected  

> select add #8/Ac:106

145008 atoms, 156353 bonds, 11286 residues, 1 model selected  

> select up

145221 atoms, 156569 bonds, 11311 residues, 1 model selected  

> select up

146892 atoms, 158273 bonds, 11521 residues, 1 model selected  

> select up

147176 atoms, 158307 bonds, 11774 residues, 1 model selected  

> select add #8/Ap:84

147187 atoms, 158317 bonds, 11775 residues, 1 model selected  

> select up

147298 atoms, 158428 bonds, 11790 residues, 1 model selected  

> select up

147884 atoms, 159025 bonds, 11865 residues, 1 model selected  

> select add #8/Aq:112

147892 atoms, 159032 bonds, 11866 residues, 1 model selected  

> select up

147968 atoms, 159108 bonds, 11875 residues, 1 model selected  

> select up

149024 atoms, 160180 bonds, 12016 residues, 1 model selected  

> select add #8/AW:103

149029 atoms, 160184 bonds, 12017 residues, 1 model selected  

> select up

149228 atoms, 160384 bonds, 12042 residues, 1 model selected  

> select up

150013 atoms, 161184 bonds, 12137 residues, 1 model selected  

> select up

150014 atoms, 161184 bonds, 12138 residues, 1 model selected  

> select ~sel & ##selected

75587 atoms, 80511 bonds, 1634 pseudobonds, 6653 residues, 3 models selected  

> color (#!8 & sel) #fffc79ff

> select ~sel & ##selected

150014 atoms, 161184 bonds, 4024 pseudobonds, 12138 residues, 3 models
selected  

> color (#!8 & sel) #76d6ffff

> select #8/Ct:366

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

> select up

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

> select up

6659 atoms, 6789 bonds, 853 residues, 1 model selected  

> select up

6691 atoms, 6823 bonds, 854 residues, 1 model selected  

> color sel forest green

> select #8/Bv:19

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

> select add #8/Bw:47

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select up

3247 atoms, 3629 bonds, 152 residues, 1 model selected  

> select up

225601 atoms, 241695 bonds, 18791 residues, 1 model selected  

> select down

3247 atoms, 3629 bonds, 152 residues, 1 model selected  

> color sel orange red

> show #!3 models

> show #!4 models

> hide #!4 models

> view matrix models
> #8,0.98772,-0.15208,0.03592,50.978,-0.070653,-0.2296,0.97072,119.64,-0.13938,-0.96133,-0.23752,515.93

> fitmap #8 inMap #3

Fit molecule 6gz5 (#8) to map MultiPostProcessor_PPout_3.mrc (#3) using 225601
atoms  
average map value = 0.7158, steps = 88  
shifted from previous position = 18.8  
rotated from previous position = 0.0276 degrees  
atoms outside contour = 62716, contour level = 0.6  
  
Position of 6gz5 (#8) relative to MultiPostProcessor_PPout_3.mrc (#3)
coordinates:  
Matrix rotation and translation  
0.98552175 -0.16444579 0.04128487 68.70940628  
-0.08050096 -0.23953489 0.96754463 118.26802312  
-0.14921947 -0.95685976 -0.24930488 510.57092206  
Axis -0.99419956 0.09841971 0.04336818  
Axis point 0.00000000 261.66236723 209.47181612  
Rotation angle (degrees) 104.57570564  
Shift along axis -34.52842622  
  

> select add #3

3247 atoms, 3629 bonds, 152 residues, 3 models selected  

> select clear

> select add #3

2 models selected  

No atoms selected for color zoning  

[Repeated 1 time(s)]

> select add #8

225601 atoms, 241695 bonds, 5658 pseudobonds, 18791 residues, 5 models
selected  

> select subtract #3

225601 atoms, 241695 bonds, 5658 pseudobonds, 18791 residues, 3 models
selected  

> color zone #3 near sel distance 24

> hide #!8 models

> color zone #3 near sel distance 12

[Repeated 2 time(s)]

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> show #!3 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!8 models

> close #2

> close #8

> close #6

> open 6hcj

Summary of feedback from opening 6hcj fetched from pdb  
---  
note | Fetching compressed mmCIF 6hcj from http://files.rcsb.org/download/6hcj.cif  
  
6hcj title:  
Structure of the rabbit 80S ribosome on globin mRNA in the rotated state with
A/P and P/E tRNAs [more info...]  
  
Chain information for 6hcj #2  
---  
Chain | Description | UniProt  
1 | nascent chain |   
33 | P/E tRNA |   
51 | 28S ribosomal RNA |   
71 | 5S ribosomal RNA |   
81 | 5.8S ribosomal RNA |   
A2 | 18S ribosomal RNA |   
A3 | Ribosomal protein L8 | G1TT27_RABIT 1-257  
B2 | uS2 |   
B3 | uL3 | G1TL06_RABIT 2-403  
C2 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264  
C3 | uL4 |   
D2 | uS5 |   
D3 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297  
E2 | uS3 | G1TNM3_RABIT 1-243  
E3 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291  
F2 | eS4 |   
F3 | uL30 | G1TUB1_RABIT 1-247  
G2 | Ribosomal protein S5 | G1TFM5_RABIT 1-204  
G3 | eL8 |   
H2 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249  
H3 | uL6 | G1TX33_RABIT 1-192  
I2 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194  
I3 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214  
J2 | eS8 |   
J3 | Ribosomal protein L11 | G1TUB8_RABIT 1-178  
K2 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194  
L2 | eS10 | G1TPV3_RABIT 1-165  
L3 | eL13 |   
M2 | Ribosomal protein S11 | G1TRM4_RABIT 1-158  
M3 | Ribosomal protein L14 | G1SZ12_RABIT 1-218  
N2 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132  
N3 | Ribosomal protein L15 | G1T0C1_RABIT 1-204  
O2 | uS15 | G1SP51_RABIT 1-151  
O3 | uL13 |   
P2 | uS11 |   
P3 | uL22 | G1TVT6_RABIT 1-184  
Q2 | uS19 | G1U0Q2_RABIT 1-145  
Q3 | eL18 |   
R2 | Ribosomal protein S16 | G1SGX4_RABIT 1-146  
R3 | eL19 |   
S2 | eS17 | G1TU13_RABIT 1-135  
S3 | eL20 |   
T2 | uS13 | G1TPG3_RABIT 1-152  
T3 | eL21 | G1SHQ2_RABIT 1-160  
U2 | eS19 |   
U3 | eL22 |   
V2 | uS10 | G1SIZ2_RABIT 1-119  
V3 | Ribosomal protein L23 | G1T6D1_RABIT 1-140  
W2 | eS21 |   
X2 | Ribosomal protein S15a | G1TG89_RABIT 1-130  
X3 | uL23 | G1SE76_RABIT 1-156  
Y2 | uS12 |   
Y3 | Ribosomal protein L26 | G1SQH0_RABIT 1-145  
Z2 | eS24 |   
Z3 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136  
a2 | eS25 | G1TDB3_RABIT 1-125  
a3 | uL15 | G1SNY0_RABIT 2-148  
b2 | eS26 |   
b3 | eL29 | G1SGR6_RABIT 1-226  
c2 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84  
c3 | eL30 | G1TDL2_RABIT 1-115  
d2 | Ribosomal protein S28 | G1TIB4_RABIT 1-69  
d3 | eL31 | G1SHG0_RABIT 1-125  
e2 | uS14 | G1U7M4_RABIT 1-56  
e3 | eL32 | G1U437_RABIT 1-135  
f2 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132  
f3 | eL33 | G1SF08_RABIT 1-110  
g2 | Ribosomal protein S27a | G1SK22_RABIT 1-156  
g3 | eL34 |   
h2 | RACK1 | G1SJB4_RABIT 1-317  
h3 | uL29 | G1SIT5_RABIT 1-123  
i3 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105  
j3 | Ribosomal protein L37 | U3KPD5_RABIT 1-97  
k3 | eL38 |   
l3 | eL39 | G1TTN1_RABIT 1-51  
m3 | eL40 |   
n3 | eL41 |   
o3 | eL42 |   
p3 | eL43 | G1SY53_RABIT 1-92  
q3 | A/P RNA |   
r3 | eL28 | G1U7L1_RABIT 1-137  
t3 | uL10 |   
u3 | Ribosomal protein L12 | G1SMR7_RABIT 1-165  
v3 | mRNA |   
w3 | uL1 | G1SKZ8_RABIT 1-217  
  
Non-standard residues in 6hcj #2  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> select #2/A2:756@C6

1 atom, 1 residue, 1 model selected  

> view matrix models #2,1,0,0,-205.34,0,1,0,-35.929,0,0,1,60.738

> show #!50 models

> hide #!50 models

> view matrix models
> #2,0.80107,-0.53914,-0.26003,67.199,0.37572,0.11474,0.9196,-121.02,-0.46596,-0.83436,0.29448,602.4

> view matrix models
> #2,-0.53044,-0.79799,0.28607,321,0.58943,-0.10466,0.80101,-78.841,-0.60926,0.59351,0.52588,167.15

> view matrix models
> #2,-0.66738,-0.7439,0.035021,406.29,0.023332,0.026117,0.99939,-30.761,-0.74436,0.66778,-7.3503e-05,319.84

> view matrix models
> #2,-0.66738,-0.7439,0.035021,458.57,0.023332,0.026117,0.99939,139.97,-0.74436,0.66778,-7.3503e-05,381.64

> view matrix models
> #2,0.20811,0.61999,0.7565,-339.09,0.66421,0.47818,-0.57461,275.3,-0.718,0.62206,-0.31229,471.88

> view matrix models
> #2,0.10791,0.55803,0.82277,-314.58,0.48253,0.69418,-0.53411,247.15,-0.8692,0.45465,-0.19436,525.2

> view matrix models
> #2,0.13833,0.92572,0.352,-301.11,0.094643,0.34143,-0.93513,550.42,-0.98585,0.16267,-0.040384,596.03

> view matrix models
> #2,0.17132,0.94637,0.27393,-294.18,0.24046,0.22947,-0.94315,548.88,-0.95542,0.22745,-0.18825,609.65

> view matrix models
> #2,0.17132,0.94637,0.27393,-327.99,0.24046,0.22947,-0.94315,368.19,-0.95542,0.22745,-0.18825,585.52

> view matrix models
> #2,0.17132,0.94637,0.27393,-150.27,0.24046,0.22947,-0.94315,363.19,-0.95542,0.22745,-0.18825,506.09

> fitmap #2 inMap #3

Fit molecule 6hcj (#2) to map MultiPostProcessor_PPout_3.mrc (#3) using 219683
atoms  
average map value = 0.7213, steps = 120  
shifted from previous position = 22.9  
rotated from previous position = 23.8 degrees  
atoms outside contour = 58481, contour level = 0.6  
  
Position of 6hcj (#2) relative to MultiPostProcessor_PPout_3.mrc (#3)
coordinates:  
Matrix rotation and translation  
0.19969064 0.96898940 -0.14554449 -39.34028625  
0.17726708 -0.18181069 -0.96722348 508.21336141  
-0.96369084 0.16734523 -0.20807582 512.21145042  
Axis 0.70588204 0.50901704 -0.49257710  
Axis point 0.00000000 89.25330235 427.63401500  
Rotation angle (degrees) 126.51961377  
Shift along axis -21.38396817  
  

> select #2/A2:1777@C2'

1 atom, 1 residue, 1 model selected  

> select clear

> hide #!2 atoms

> show #!2 cartoons

> hide #!3 models

Drag select of 5604 residues, 4 pseudobonds  

> select up

116863 atoms, 127373 bonds, 4 pseudobonds, 8009 residues, 2 models selected  

> select up

124888 atoms, 135571 bonds, 4 pseudobonds, 8983 residues, 2 models selected  
Drag select of 8723 residues, 7 pseudobonds  

> select up

133961 atoms, 145116 bonds, 7 pseudobonds, 9874 residues, 2 models selected  

> select up

140205 atoms, 151473 bonds, 7 pseudobonds, 10661 residues, 2 models selected  

> select ~sel & ##selected

79478 atoms, 84304 bonds, 1501 pseudobonds, 7285 residues, 4 models selected  

> select subtract /p3

78769 atoms, 83585 bonds, 1500 pseudobonds, 7193 residues, 4 models selected  

> select subtract /c3

78008 atoms, 82814 bonds, 1500 pseudobonds, 7095 residues, 4 models selected  

> select subtract /u3

76848 atoms, 81640 bonds, 1500 pseudobonds, 6942 residues, 4 models selected  

> color (#!2 & sel) #fffc79ff

> select ~sel & ##selected

142835 atoms, 154137 bonds, 2475 pseudobonds, 11004 residues, 4 models
selected  

> color (#!2 & sel) #76d6ffff

> select #2/33:51

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #2/q3:22

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select up

3183 atoms, 3560 bonds, 149 residues, 1 model selected  

> color sel orange red

> show #!3 models

> select add #2

219683 atoms, 235777 bonds, 3975 pseudobonds, 17946 residues, 4 models
selected  

> show #!59 models

> hide #!3 models

> hide #!59 models

> show #!61 models

> select add #61/eEF2:91

219692 atoms, 235785 bonds, 3975 pseudobonds, 17947 residues, 5 models
selected  

> select up

219809 atoms, 235902 bonds, 3975 pseudobonds, 17962 residues, 5 models
selected  

> select up

226252 atoms, 242472 bonds, 3975 pseudobonds, 18788 residues, 5 models
selected  

> hide #!61 models

> show #!3 models

> color zone #3 near sel distance 12

> hide #!2 models

> show #!4 models

> show #!5 models

> hide #!4 models

> hide #!5 models

> hide #!3 models

> select subtract #2

6569 atoms, 6695 bonds, 842 residues, 1 model selected  

> show #!4 models

> show #!5 models

> hide #!4 models

> show #!4 models

> open 6tnu

6tnu title:  
Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs.
[more info...]  
  
Chain information for 6tnu #6  
---  
Chain | Description | UniProt  
2 | 18S rRNA |   
A | 40S ribosomal protein S3 | RS3_YEAST 4-225  
AA | 60S ribosomal protein L8-A | RL8A_YEAST 24-256  
AB | 60S ribosomal protein L23-A | RL23A_YEAST 2-137  
AC | 60S ribosomal protein L36-A | RL36A_YEAST 2-100  
AD | 60S ribosomal protein L9-A | RL9A_YEAST 1-191  
AE | 60S ribosomal protein L24-A | RL24A_YEAST 1-126  
AF | 60S ribosomal protein L37-A | RL37A_YEAST 2-82  
AG | 60S ribosomal protein L11-B | RL11B_YEAST 6-174  
AH | 60S ribosomal protein L25 | RL25_YEAST 22-142  
AI | 60S ribosomal protein L38 | RL38_YEAST 2-78  
AJ | 60S ribosomal protein L13-A | RL13A_YEAST 2-194  
AK | 60S ribosomal protein L26-A | RL26A_YEAST 2-126  
AL | 60S ribosomal protein L39 | RL39_YEAST 2-51  
AM | 60S ribosomal protein L14-A | RL14A_YEAST 3-138  
AN | 60S ribosomal protein L27-A | RL27A_YEAST 2-136  
AO | Ubiquitin-60S ribosomal protein L40 | RL40A_YEAST 77-128  
AP | 60S ribosomal protein L42-A | RL44A_YEAST 2-104  
AQ | 60S ribosomal protein L15-A | RL15A_YEAST 2-204  
AR | 60S ribosomal protein L28 | RL28_YEAST 2-149  
AS | 60S ribosomal protein L41-A |   
AT | 60S ribosomal protein L43-A | RL43A_YEAST 2-92  
AU | 60S ribosomal protein L16-A | RL16A_YEAST 3-199  
AV | 60S ribosomal protein L29 | RL29_YEAST 2-59  
AW | 60S ribosomal protein L2-A | RL2A_YEAST 2-252  
AX | 60S ribosomal protein L17-A | RL17A_YEAST 2-184  
AY | 60S ribosomal protein L30 | RL30_YEAST 9-104  
B | Rps5p | A0A1L4AA68_YEASX 20-225  
BA | 60S ribosomal protein L3 | RL3_YEAST 2-387  
BB | 60S ribosomal protein L18-A | RL18A_YEAST 2-186  
BC | 60S ribosomal protein L31-A | RL31A_YEAST 4-112  
BD | 60S ribosomal protein L10 | RL10_YEAST 2-219  
BE | 60S ribosomal protein L4-A | RL4A_YEAST 2-362  
BF | 60S ribosomal protein L19-A | RL19A_YEAST 2-189  
BG | 60S ribosomal protein L32 | RL32_YEAST 2-128  
BH | 60S ribosomal protein L20-A | RL20A_YEAST 2-172  
BI | 60S ribosomal protein L5 | RL5_YEAST 4-297  
BJ | 60S ribosomal protein L21-A | RL21A_YEAST 2-160  
BK | 60S ribosomal protein L33-A | RL33A_YEAST 2-107  
BL | 60S ribosomal protein L22-A | RL22A_YEAST 9-108  
BM | 60S ribosomal protein L6-B | RL6B_YEAST 2-176  
BN | 60S ribosomal protein L34-A | RL34A_YEAST 2-113  
BO | 60S ribosomal protein L7-A | RL7A_YEAST 23-244  
BP | 60S ribosomal protein L35-A | RL35A_YEAST 2-120  
BQ | 25S rRNA |   
BR | 5S rRNA |   
BS | 5.8S rRNA |   
BT | 60S ribosomal protein L1 |   
C | 40S ribosomal protein S10-A | RS10A_YEAST 1-92  
D | 40S ribosomal protein S12 | RS12_YEAST 23-143  
E | 40S ribosomal protein S15 | RS15_YEAST 13-129  
F | 40S ribosomal protein S16-A | RS16A_YEAST 3-143  
G | 40S ribosomal protein S17-B | RS17B_YEAST 2-126  
H | 40S ribosomal protein S18-A | RS18A_YEAST 2-146  
I | 40S ribosomal protein S19-A | RS19A_YEAST 2-144  
J | 40S ribosomal protein S20 | RS20_YEAST 20-119  
K | 40S ribosomal protein S25-A | RS25A_YEAST 24-105  
L | 40S ribosomal protein S28-A | RS28A_YEAST 5-67  
M | 40S ribosomal protein S29-A | RS29A_YEAST 4-56  
N | Ubiquitin-40S ribosomal protein S31 | RS31_YEAST 80-152  
O | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 5-316  
P | 40S ribosomal protein S0-A | RSSA1_YEAS1 2-207  
Q | 40S ribosomal protein S1-A | RS3A1_YEAS1 2-233  
R | 40S ribosomal protein S2 | RS2_YEAST 34-249  
S | 40S ribosomal protein S4-A | RS4A_YEAST 2-259  
T | 40S ribosomal protein S6-A | RS6A_YEAST 1-228  
U | 40S ribosomal protein S7-A | RS7A_YEAST 4-187  
V | 40S ribosomal protein S8 | A0A0J9X221_LACKL 2-199  
W | 40S ribosomal protein S9-A | RS9A_YEAST 2-185  
X | 40S ribosomal protein S11-A | RS11A_YEAST 4-145  
Y | 40S ribosomal protein S13 | RS13_YEAST 2-151  
Z | 40S ribosomal protein S14-B | RS14B_YEAST 11-137  
a | 40S ribosomal protein S21-A | RS21A_YEAST 1-87  
b | 40S ribosomal protein S22-A | RS22A_YEAST 2-130  
c | 40S ribosomal protein S23-A | RS23A_YEAST 2-145  
d | 40S ribosomal protein S24-A | RS24A_YEAST 2-135  
e | 40S ribosomal protein S26-B | RS26B_YEAST 2-98  
eI | Eukaryotic translation initiation factor 5A-1 | IF5A1_YEAST 4-157  
f | 40S ribosomal protein S27-A | RS27A_YEAST 2-82  
g | 40S ribosomal protein S30-A | RS30A_YEAST 2-61  
l | mRNA |   
m | A-site tRNA |   
n | P-site tRNA |   
  
Non-standard residues in 6tnu #6  
---  
3HE —
4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
ZN — zinc ion  
  
1555 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select #6/2:840@C1'

1 atom, 1 residue, 1 model selected  

> view matrix models #6,1,0,0,148.51,0,1,0,44.76,0,0,1,-71.245

> view matrix models
> #6,0.82699,0.48535,-0.28378,131.56,-0.15213,-0.29275,-0.94401,669.7,-0.54125,0.82385,-0.16826,134.16

> view matrix models
> #6,0.35749,0.55763,-0.74917,345.81,-0.58021,-0.49597,-0.64603,756.33,-0.73181,0.66563,0.14624,145.35

> view matrix models
> #6,0.24674,0.79629,-0.55231,259.31,-0.51837,-0.37309,-0.76948,738.71,-0.81878,0.47616,0.32072,174.4

> view matrix models
> #6,0.063229,0.97464,-0.21466,171.85,-0.47311,-0.16011,-0.86633,694.16,-0.87873,0.15633,0.45098,243.12

> view matrix models
> #6,0.086698,0.92161,-0.37832,221.5,-0.31669,-0.33456,-0.88757,707.78,-0.94456,0.19676,0.26286,295.85

> close #6

> open 5lzs

5lzs title:  
Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA,
eEF1A, and didemnin B [more info...]  
  
Chain information for 5lzs #6  
---  
Chain | Description | UniProt  
2 ii | tRNA |   
3 | E-site tRNA |   
5 | 28S ribosomal RNA |   
7 | 5S ribosomal RNA |   
8 | 5.8S ribosomal RNA |   
9 | 18S ribosomal RNA |   
A | uL2 | G1TT27_RABIT 1-257  
AA | uS2 |   
B | uL3 | G1TL06_RABIT 2-403  
BB | 40S ribosomal protein S3a | G1SS70_RABIT 1-264  
C | uL4 | G1SVW5_RABIT 1-378  
CC | uS5 |   
D | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297  
DD | uS4 | G1TNM3_RABIT 1-243  
E | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291  
EE | 40S ribosomal protein S4 |   
F | uL30 | G1TUB1_RABIT 1-247  
FF | Uncharacterized protein | G1TFM5_RABIT 1-204  
G | eL8 | G1STW0_RABIT 78-319  
GG | 40S ribosomal protein S6 | G1TM55_RABIT 1-249  
H | uL6 | G1TX33_RABIT 1-192  
HH | uS7 | G1SVB0_RABIT 1-194  
I | Ribosomal protein L10 (Predicted) | B7NZQ2_RABIT 1-214  
II | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208  
J | uL5 | G1TUB8_RABIT 1-178  
JJ | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194  
KK | eS10 | G1TPV3_RABIT 1-165  
L | eL13 |   
LL | uS17 | G1TRM4_RABIT 1-158  
M | eL14 | G1SZ12_RABIT 1-218  
MM | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132  
N | Ribosomal protein L15 | G1T0C1_RABIT 1-204  
NN | uS15 | G1SP51_RABIT 1-151  
O | uL13 |   
OO | uS11 | G1T1F0_RABIT -4-151  
P | uL22 | G1TVT6_RABIT 1-184  
PP | uS19 | G1U0Q2_RABIT 1-145  
Q | eL18 |   
QQ | uS9 | G1SGX4_RABIT 1-146  
R | eL19 |   
RR | eS17 | G1TU13_RABIT 1-135  
S | eL20 |   
SS | uS13 | G1TPG3_RABIT 1-152  
T | eL21 | G1SHQ2_RABIT 1-160  
TT | eS19 | G1TN62_RABIT 1-145  
U | eL22 |   
UU | uS10 | G1SIZ2_RABIT 1-119  
V | uL14 | G1T6D1_RABIT 1-140  
VV | eS21 |   
W | uL24 | G1SE28_RABIT 1-157  
WW | uS8 | G1TG89_RABIT 1-130  
X | uL23 | G1SE76_RABIT 1-156  
XX | uS12 |   
Y | uL24 | G1SQH0_RABIT 1-145  
YY | eS24 |   
Z | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136  
ZZ | eS25 | G1TDB3_RABIT 1-125  
a | uL15 | G1SNY0_RABIT 1-148  
aa | eS26 |   
b | eL29 | G1SGR6_RABIT 1-226  
bb | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84  
c | eL30 | G1TDL2_RABIT 1-115  
cc | eS28 | G1TIB4_RABIT 1-69  
d | eL31 | G1SHG0_RABIT 1-125  
dd | uS14 | G1U7M4_RABIT 1-56  
e | eL32 | G1U437_RABIT 1-135  
ee | eS30 | G1T8A2_RABIT 0-132  
f | eL33 | G1SF08_RABIT 1-110  
ff | eS31 | G1SK22_RABIT 1-156  
g | eL34 | G1U945_RABIT 1-116  
gg | RACK1 | G1SJB4_RABIT 1-317  
h | uL29 | G1SIT5_RABIT 1-123  
hh | mRNA |   
i | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105  
j | Ribosomal protein L37 | U3KPD5_RABIT 1-97  
jj | Elongation factor 1-alpha 1 | EF1A1_RABIT 1-462  
k | eL38 |   
l | eL39 | G1TTN1_RABIT 1-51  
m | eL40 |   
n | 60s ribosomal protein l41 |   
o | eL42 | G1U344_RABIT 1-106  
p | eL43 | G1SY53_RABIT 1-92  
r | eL28 | G1U7L1_RABIT 1-137  
s | uL10 |   
t | uL11 | G1SMR7_RABIT 1-165  
  
Non-standard residues in 5lzs #6  
---  
7C4 —
(2~{S})-~{N}-[(2~{R})-1-[[(3~{S},6~{S},8~{S},12~{S},13~{R},16~{S},17~{R},20~{S},23~{S})-13-[(2~{S})-butan-2-yl]-20-[(4-methoxyphenyl)methyl]-6,17,21-trimethyl-3-(2-methylpropyl)-12-oxidanyl-2,5,7,10,15,19,22-heptakis(oxidanylidene)-8-propan-2-yl-9,18-dioxa-1,4,14,21-tetrazabicyclo[21.3.0]hexacosan-16-yl]amino]-4-methyl-1-oxidanylidene-
pentan-2-yl]-~{N}-methyl-1-[(2~{S})-2-oxidanylpropanoyl]pyrrolidine-2-carboxamide  
GDP — guanosine-5'-diphosphate  
MG — magnesium ion  
ZN — zinc ion  
  

> select #6/9:199@C4'

1 atom, 1 residue, 1 model selected  

> view matrix models #6,1,0,0,57.322,0,1,0,12.981,0,0,1,-21.179

> view matrix models
> #6,0.16633,0.88568,-0.43349,134.4,0.024936,-0.44325,-0.89605,679.37,-0.98576,0.13823,-0.095809,499.01

> view matrix models
> #6,0.16633,0.88568,-0.43349,74.963,0.024936,-0.44325,-0.89605,650.37,-0.98576,0.13823,-0.095809,543.83

> view matrix models
> #6,0.16633,0.88568,-0.43349,96.518,0.024936,-0.44325,-0.89605,629.39,-0.98576,0.13823,-0.095809,515.36

> view matrix models
> #6,0.16633,0.88568,-0.43349,63.252,0.024936,-0.44325,-0.89605,614.05,-0.98576,0.13823,-0.095809,517.57

> hide #!4 models

> show #!4 models

> hide #!5 models

> fitmap #6 inMap #4

Fit molecule 5lzs (#6) to map MultiPostProcessor_PPout_6.mrc (#4) using 220934
atoms  
average map value = 0.8005, steps = 104  
shifted from previous position = 9.98  
rotated from previous position = 16.3 degrees  
atoms outside contour = 40809, contour level = 0.6  
  
Position of 5lzs (#6) relative to MultiPostProcessor_PPout_6.mrc (#4)
coordinates:  
Matrix rotation and translation  
0.16548127 0.97224924 -0.16537042 -35.07168013  
0.16376994 -0.19244476 -0.96754557 525.04887214  
-0.97252011 0.13302796 -0.19107121 532.40698350  
Axis 0.69379307 0.50882094 -0.50965912  
Axis point 0.00000000 91.40984601 445.00294603  
Rotation angle (degrees) 127.51848480  
Shift along axis -28.52269859  
  

> hide #!4 models

> select clear

> hide #!6 atoms

> show #!6 cartoons

Drag select of 5254 residues, 1 pseudobonds  
Drag select of 8720 residues, 7 pseudobonds  

> select up

131239 atoms, 142165 bonds, 7 pseudobonds, 9661 residues, 2 models selected  

> select up

137761 atoms, 148800 bonds, 7 pseudobonds, 10497 residues, 2 models selected  

> select ~sel & ##selected

83173 atoms, 88152 bonds, 2044 pseudobonds, 7689 residues, 4 models selected  

> select subtract /p

82464 atoms, 87434 bonds, 2040 pseudobonds, 7597 residues, 4 models selected  

> select subtract /c

81703 atoms, 86663 bonds, 2040 pseudobonds, 7499 residues, 4 models selected  

> color (#!6 & sel) #fffc79ff

> select ~sel & ##selected

139231 atoms, 150289 bonds, 3847 pseudobonds, 10687 residues, 4 models
selected  

> color (#!6 & sel) #76d6ffff

> show #!4 models

> hide #!4 models

> select #6/jj:114

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

> select up

46 atoms, 45 bonds, 7 residues, 1 model selected  

> select up

3383 atoms, 3453 bonds, 441 residues, 1 model selected  

> select up

3491 atoms, 3565 bonds, 444 residues, 1 model selected  

> color sel #d783ffff

> color sel #ff85ffff

> color sel #9437ffff

> color sel #ff40ffff

> color sel #7a81ffff

> color sel #d783ffff

> select #6/ii:22

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

> select add #6/2:25

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #6/3:46

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select up

4825 atoms, 5391 bonds, 227 residues, 1 model selected  

> color sel orange red

> show #!58 models

> hide #!58 models

> show #!60 models

> hide #!60 models

> show #!61 models

> hide #!61 models

> show #!2 models

> select add #6

220934 atoms, 236952 bonds, 5887 pseudobonds, 18186 residues, 4 models
selected  

> select #2/51:4040

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

> select add #6

220954 atoms, 236973 bonds, 5887 pseudobonds, 18187 residues, 5 models
selected  

> select up

298761 atoms, 324023 bonds, 5887 pseudobonds, 21821 residues, 5 models
selected  

> select up

298961 atoms, 324023 bonds, 5887 pseudobonds, 22021 residues, 5 models
selected  

> select down

298761 atoms, 324023 bonds, 5887 pseudobonds, 21821 residues, 5 models
selected  

> select subtract #2/33

298761 atoms, 324023 bonds, 5887 pseudobonds, 21821 residues, 5 models
selected  

> hide #!6 models

> show #!6 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> color zone #3 near sel distance 12

> undo

> hide #!3 models

> show #!4 models

> color zone #4 near sel distance 8

> undo

> color zone #4 near sel distance 8

> show #!2 models

> select add #2/w3:148

298768 atoms, 324029 bonds, 5887 pseudobonds, 21822 residues, 5 models
selected  

> select up

298806 atoms, 324067 bonds, 5887 pseudobonds, 21827 residues, 5 models
selected  

> select up

300502 atoms, 325792 bonds, 5887 pseudobonds, 22038 residues, 5 models
selected  

> color zone #4 near sel distance 8

> hide #!6 models

> hide #!4 models

> hide #!2 models

> select clear

> show #!3 models

> show #!4 models

> show #!5 models

> hide #!4 models

> hide #!3 models

> hide #!5 models

> show #!5 models

> show #!4 models

> show #!3 models

> volume #3-5 level 0.7

> volume #3-5 level 0.65

> volume #3-5 level 0.6

> hide #!4 models

> volume #3-5 level 0.7

> volume #3-5 level 0.65

> show #!4 models

> save /Users/campbell/Desktop/Chimera_sessions/subunit_colouring.cxs
> includeMaps true

——— End of log from Thu Sep 12 05:33:16 2024 ———

opened ChimeraX session  

> open 6tnu

6tnu title:  
Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs.
[more info...]  
  
Chain information for 6tnu #7  
---  
Chain | Description | UniProt  
2 | 18S rRNA |   
A | 40S ribosomal protein S3 | RS3_YEAST 4-225  
AA | 60S ribosomal protein L8-A | RL8A_YEAST 24-256  
AB | 60S ribosomal protein L23-A | RL23A_YEAST 2-137  
AC | 60S ribosomal protein L36-A | RL36A_YEAST 2-100  
AD | 60S ribosomal protein L9-A | RL9A_YEAST 1-191  
AE | 60S ribosomal protein L24-A | RL24A_YEAST 1-126  
AF | 60S ribosomal protein L37-A | RL37A_YEAST 2-82  
AG | 60S ribosomal protein L11-B | RL11B_YEAST 6-174  
AH | 60S ribosomal protein L25 | RL25_YEAST 22-142  
AI | 60S ribosomal protein L38 | RL38_YEAST 2-78  
AJ | 60S ribosomal protein L13-A | RL13A_YEAST 2-194  
AK | 60S ribosomal protein L26-A | RL26A_YEAST 2-126  
AL | 60S ribosomal protein L39 | RL39_YEAST 2-51  
AM | 60S ribosomal protein L14-A | RL14A_YEAST 3-138  
AN | 60S ribosomal protein L27-A | RL27A_YEAST 2-136  
AO | Ubiquitin-60S ribosomal protein L40 | RL40A_YEAST 77-128  
AP | 60S ribosomal protein L42-A | RL44A_YEAST 2-104  
AQ | 60S ribosomal protein L15-A | RL15A_YEAST 2-204  
AR | 60S ribosomal protein L28 | RL28_YEAST 2-149  
AS | 60S ribosomal protein L41-A |   
AT | 60S ribosomal protein L43-A | RL43A_YEAST 2-92  
AU | 60S ribosomal protein L16-A | RL16A_YEAST 3-199  
AV | 60S ribosomal protein L29 | RL29_YEAST 2-59  
AW | 60S ribosomal protein L2-A | RL2A_YEAST 2-252  
AX | 60S ribosomal protein L17-A | RL17A_YEAST 2-184  
AY | 60S ribosomal protein L30 | RL30_YEAST 9-104  
B | Rps5p | A0A1L4AA68_YEASX 20-225  
BA | 60S ribosomal protein L3 | RL3_YEAST 2-387  
BB | 60S ribosomal protein L18-A | RL18A_YEAST 2-186  
BC | 60S ribosomal protein L31-A | RL31A_YEAST 4-112  
BD | 60S ribosomal protein L10 | RL10_YEAST 2-219  
BE | 60S ribosomal protein L4-A | RL4A_YEAST 2-362  
BF | 60S ribosomal protein L19-A | RL19A_YEAST 2-189  
BG | 60S ribosomal protein L32 | RL32_YEAST 2-128  
BH | 60S ribosomal protein L20-A | RL20A_YEAST 2-172  
BI | 60S ribosomal protein L5 | RL5_YEAST 4-297  
BJ | 60S ribosomal protein L21-A | RL21A_YEAST 2-160  
BK | 60S ribosomal protein L33-A | RL33A_YEAST 2-107  
BL | 60S ribosomal protein L22-A | RL22A_YEAST 9-108  
BM | 60S ribosomal protein L6-B | RL6B_YEAST 2-176  
BN | 60S ribosomal protein L34-A | RL34A_YEAST 2-113  
BO | 60S ribosomal protein L7-A | RL7A_YEAST 23-244  
BP | 60S ribosomal protein L35-A | RL35A_YEAST 2-120  
BQ | 25S rRNA |   
BR | 5S rRNA |   
BS | 5.8S rRNA |   
BT | 60S ribosomal protein L1 |   
C | 40S ribosomal protein S10-A | RS10A_YEAST 1-92  
D | 40S ribosomal protein S12 | RS12_YEAST 23-143  
E | 40S ribosomal protein S15 | RS15_YEAST 13-129  
F | 40S ribosomal protein S16-A | RS16A_YEAST 3-143  
G | 40S ribosomal protein S17-B | RS17B_YEAST 2-126  
H | 40S ribosomal protein S18-A | RS18A_YEAST 2-146  
I | 40S ribosomal protein S19-A | RS19A_YEAST 2-144  
J | 40S ribosomal protein S20 | RS20_YEAST 20-119  
K | 40S ribosomal protein S25-A | RS25A_YEAST 24-105  
L | 40S ribosomal protein S28-A | RS28A_YEAST 5-67  
M | 40S ribosomal protein S29-A | RS29A_YEAST 4-56  
N | Ubiquitin-40S ribosomal protein S31 | RS31_YEAST 80-152  
O | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 5-316  
P | 40S ribosomal protein S0-A | RSSA1_YEAS1 2-207  
Q | 40S ribosomal protein S1-A | RS3A1_YEAS1 2-233  
R | 40S ribosomal protein S2 | RS2_YEAST 34-249  
S | 40S ribosomal protein S4-A | RS4A_YEAST 2-259  
T | 40S ribosomal protein S6-A | RS6A_YEAST 1-228  
U | 40S ribosomal protein S7-A | RS7A_YEAST 4-187  
V | 40S ribosomal protein S8 | A0A0J9X221_LACKL 2-199  
W | 40S ribosomal protein S9-A | RS9A_YEAST 2-185  
X | 40S ribosomal protein S11-A | RS11A_YEAST 4-145  
Y | 40S ribosomal protein S13 | RS13_YEAST 2-151  
Z | 40S ribosomal protein S14-B | RS14B_YEAST 11-137  
a | 40S ribosomal protein S21-A | RS21A_YEAST 1-87  
b | 40S ribosomal protein S22-A | RS22A_YEAST 2-130  
c | 40S ribosomal protein S23-A | RS23A_YEAST 2-145  
d | 40S ribosomal protein S24-A | RS24A_YEAST 2-135  
e | 40S ribosomal protein S26-B | RS26B_YEAST 2-98  
eI | Eukaryotic translation initiation factor 5A-1 | IF5A1_YEAST 4-157  
f | 40S ribosomal protein S27-A | RS27A_YEAST 2-82  
g | 40S ribosomal protein S30-A | RS30A_YEAST 2-61  
l | mRNA |   
m | A-site tRNA |   
n | P-site tRNA |   
  
Non-standard residues in 6tnu #7  
---  
3HE —
4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
ZN — zinc ion  
  
1555 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select #7/R:58@CD2

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #7,1,0,0,92.926,0,1,0,123.36,0,0,1,-0.21597

> view matrix models
> #7,-0.018958,0.9998,-0.0064026,77.573,-0.14881,-0.0091539,-0.98882,682,-0.98868,-0.017793,0.14895,464.55

> view matrix models
> #7,-0.018958,0.9998,-0.0064026,-14.944,-0.14881,-0.0091539,-0.98882,548.82,-0.98868,-0.017793,0.14895,477.57

> fitmap #7 inMap #50

Fit molecule 6tnu (#7) to map Stable_60S.mrc (#50) using 204962 atoms  
average map value = 0.5466, steps = 112  
shifted from previous position = 9.4  
rotated from previous position = 9.88 degrees  
atoms outside contour = 89971, contour level = 0.6  
  
Position of 6tnu (#7) relative to Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.15001217 0.98856074 0.01562163 -55.93626098  
-0.12363146 0.03443256 -0.99173065 526.76497245  
-0.98092387 0.14684034 0.12738251 442.08316198  
Axis 0.60630786 0.53067694 -0.59226072  
Axis point 0.00000000 38.71208624 502.13571468  
Rotation angle (degrees) 110.12603468  
Shift along axis -16.20106278  
  

> show #!58 models

> hide #!58 models

> hide #!7 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> show #!1 models

> show #!58 models

> hide #!58 models

> show #!58 models

> show #!59 models

> hide #!58 models

> show #!58 models

> show #!61 models

> hide #!59 models

> hide #!58 models

> show #!7 models

> hide sel atoms

> show sel cartoons

> select clear

> hide #!7,61 atoms

> show #!7,61 cartoons

> select #7/eI:138

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

> select up

57 atoms, 56 bonds, 8 residues, 1 model selected  

> select up

1143 atoms, 1158 bonds, 154 residues, 1 model selected  

> select ~sel & ##selected

203819 atoms, 219024 bonds, 5230 pseudobonds, 16744 residues, 4 models
selected  

> hide sel cartoons

> select ~sel & ##selected

1143 atoms, 1158 bonds, 154 residues, 1 model selected  

> select #61/PSIT:45

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

> select up

1644 atoms, 1836 bonds, 77 residues, 1 model selected  

> select up

1650 atoms, 1836 bonds, 83 residues, 1 model selected  

> select up

207066 atoms, 221714 bonds, 17603 residues, 1 model selected  

> select down

1650 atoms, 1836 bonds, 83 residues, 1 model selected  

> color sel #76d6ffff

> select add #61

207066 atoms, 221714 bonds, 5069 pseudobonds, 17603 residues, 4 models
selected  

> select #7/eI:91

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

> select up

38 atoms, 38 bonds, 4 residues, 1 model selected  

> select up

1143 atoms, 1158 bonds, 154 residues, 1 model selected  

> select add #61

208209 atoms, 222872 bonds, 5069 pseudobonds, 17757 residues, 5 models
selected  

> select subtract /PSIT

206559 atoms, 221036 bonds, 4995 pseudobonds, 17674 residues, 5 models
selected  

> select subtract /aSIT

206559 atoms, 221036 bonds, 4995 pseudobonds, 17674 residues, 5 models
selected  

> ui tool show "Color Zone"

> color zone #1 near #61 distance 4

> color zone #1 near sel distance 4

> color zone #1 near sel distance 12

> color zone #1 near sel distance 20

[Repeated 1 time(s)]

> color zone #1 near sel distance 21

> color zone #1 near sel distance 22

> color zone #1 near sel distance 23

> color zone #1 near sel distance 24

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select add #7

410378 atoms, 440060 bonds, 10225 pseudobonds, 34418 residues, 8 models
selected  

> select add #61

412028 atoms, 441896 bonds, 10299 pseudobonds, 34501 residues, 8 models
selected  

> select subtract #61

204962 atoms, 220182 bonds, 5230 pseudobonds, 16898 residues, 4 models
selected  

> show sel cartoons

> select #7/BT:140

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

> select up

60 atoms, 59 bonds, 12 residues, 1 model selected  

> select up

1050 atoms, 1049 bonds, 210 residues, 1 model selected  

> select up

204962 atoms, 220182 bonds, 16898 residues, 1 model selected  

> select down

1050 atoms, 1049 bonds, 210 residues, 1 model selected  

> color sel #7a81ffff

> color sel #76d6ffff

> select #7/eI:151

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

> select add #61/ASIT:40

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

> select up

1707 atoms, 1898 bonds, 85 residues, 2 models selected  

> select up

2779 atoms, 2985 bonds, 230 residues, 2 models selected  

> select up

2780 atoms, 2985 bonds, 231 residues, 2 models selected  

> select add #7/BT:140

2785 atoms, 2989 bonds, 232 residues, 2 models selected  

> select up

2840 atoms, 3044 bonds, 243 residues, 2 models selected  

> select up

3830 atoms, 4034 bonds, 441 residues, 2 models selected  

> select ~sel & ##selected

408198 atoms, 437862 bonds, 10264 pseudobonds, 34060 residues, 8 models
selected  

> hide sel cartoons

> hide #!61 models

> show #!61 models

> select add #61

409835 atoms, 439689 bonds, 10299 pseudobonds, 34137 residues, 8 models
selected  

> select add #7/BT:139

409840 atoms, 439693 bonds, 10299 pseudobonds, 34138 residues, 8 models
selected  

> select add #7/eI:140

409846 atoms, 439698 bonds, 10299 pseudobonds, 34139 residues, 8 models
selected  

> select up

409952 atoms, 439804 bonds, 10299 pseudobonds, 34157 residues, 8 models
selected  

> select up

412028 atoms, 441896 bonds, 10299 pseudobonds, 34501 residues, 8 models
selected  

> select subtract /ASIT

410391 atoms, 440069 bonds, 10250 pseudobonds, 34424 residues, 8 models
selected  

> color zone #1 near sel distance 24

> select subtract #7

205429 atoms, 219887 bonds, 5020 pseudobonds, 17526 residues, 4 models
selected  

> select add #7/BT:140

205434 atoms, 219891 bonds, 5020 pseudobonds, 17527 residues, 7 models
selected  

> select add #7/eI:139

205442 atoms, 219898 bonds, 5020 pseudobonds, 17528 residues, 7 models
selected  

> select up

205546 atoms, 220002 bonds, 5020 pseudobonds, 17546 residues, 7 models
selected  

> select up

207622 atoms, 222094 bonds, 5020 pseudobonds, 17890 residues, 7 models
selected  

> color zone #1 near sel distance 24

> lighting simple

> select #7/eI:45

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

> select up

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

> select up

1143 atoms, 1158 bonds, 154 residues, 1 model selected  

> color sel #7a81ffff

> color sel #d783ffff

> color sel #0433ffff

> color sel #7a81ffff

> color sel #d783ffff

> color sel #ff85ffff

> color sel #d783ffff

> color sel #7a81ffff

> select add #7/BT:69

1148 atoms, 1162 bonds, 155 residues, 1 model selected  

> select up

1198 atoms, 1212 bonds, 165 residues, 1 model selected  

> select up

2193 atoms, 2207 bonds, 364 residues, 1 model selected  

> select add #61

209259 atoms, 223921 bonds, 5069 pseudobonds, 17967 residues, 5 models
selected  

> select subtract /ASIT

207622 atoms, 222094 bonds, 5020 pseudobonds, 17890 residues, 5 models
selected  

> color zone #1 near sel distance 24

> show sel cartoons

> select subtract /PSIT

205972 atoms, 220258 bonds, 4946 pseudobonds, 17807 residues, 5 models
selected  

> color zone #1 near sel distance 24

> show #!58 models

> select add #58/12:32

205980 atoms, 220265 bonds, 4946 pseudobonds, 17808 residues, 6 models
selected  

> select up

206042 atoms, 220328 bonds, 4946 pseudobonds, 17816 residues, 6 models
selected  

> select up

206907 atoms, 221201 bonds, 4946 pseudobonds, 17931 residues, 6 models
selected  

> select up

621164 atoms, 666615 bonds, 5069 pseudobonds, 51583 residues, 6 models
selected  

> color zone #1 near sel distance 24

> select down

206907 atoms, 221201 bonds, 4946 pseudobonds, 17931 residues, 6 models
selected  

> select subtract /1S

206907 atoms, 221201 bonds, 4946 pseudobonds, 17931 residues, 6 models
selected  

> select subtract /12

205972 atoms, 220258 bonds, 4946 pseudobonds, 17807 residues, 5 models
selected  

> hide #!7 models

> hide #!58 models

> hide #!61 models

> select add #61

209259 atoms, 223921 bonds, 5069 pseudobonds, 17967 residues, 5 models
selected  

> select add #7

412028 atoms, 441896 bonds, 10299 pseudobonds, 34501 residues, 8 models
selected  

> select subtract #61

204962 atoms, 220182 bonds, 5230 pseudobonds, 16898 residues, 4 models
selected  

> select subtract #7

Nothing selected  

> hide #!1 models

> show #!1 models

> show #!58 models

> select add #58/1S:1225

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

> show #!7 models

> select add #7/BT:70

25 atoms, 25 bonds, 2 residues, 2 models selected  

> select add #7/eI:138

33 atoms, 32 bonds, 3 residues, 2 models selected  

> select up

38061 atoms, 42555 bonds, 1800 residues, 2 models selected  

> select up

40142 atoms, 44652 bonds, 2145 residues, 2 models selected  

> show #!61 models

> select add #61

247208 atoms, 266366 bonds, 5069 pseudobonds, 19748 residues, 6 models
selected  

> select subtract /ASIT

245571 atoms, 264539 bonds, 5020 pseudobonds, 19671 residues, 6 models
selected  

> select subtract /PSIT

243921 atoms, 262703 bonds, 4946 pseudobonds, 19588 residues, 6 models
selected  

> color zone #1 near sel distance 24

> hide #!7 models

> hide #!58 models

> hide #!61 models

> volume #1 level 0.7334

> volume #1 level 0.77

> volume level 0.77

> show #!3 models

> hide #!1 models

> volume level 0.7

> volume level 0.65

> volume level 0.66

> volume level 0.

> volume level 0.6

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!4 models

> show #!5 models

> hide #!5 models

> hide #!4 models

> show #!1 models

> volume #1 level 0.6627

> volume #1 level 0.6

> volume #1 level 0.7

> volume #1 level 0.75

> hide #!3 models

> show #!3 models

> hide #!3 models

> volume #1 level 0.6

> show #!3 models

> hide #!1 models

> volume level 0.65

> show #!1 models

> hide #!3 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!4 models

> show #!1 models

> hide #!4 models

> show #!3 models

> hide #!1 models

> show #!4 models

> hide #!3 models

> show #!5 models

> show #!3 models

> hide #!4 models

> hide #!3 models

> hide #!5 models

> show #!3 models

> show #!4 models

> hide #!3 models

> show #!6 models

> select clear

> select add #4

2 models selected  

> select subtract /3

2 models selected  

> select subtract /3

2 models selected  

> select subtract #6/3

2 models selected  

> select subtract \3

Expected an objects specifier or a keyword  

> select subtract /3

2 models selected  

> select clear

> select #6

220934 atoms, 236952 bonds, 5887 pseudobonds, 18186 residues, 4 models
selected  

> log metadata #6

No models had metadata

> log chains #6

Chain information for 5lzs #6  
---  
Chain | Description | UniProt  
2 ii | tRNA |   
3 | E-site tRNA |   
5 | 28S ribosomal RNA |   
7 | 5S ribosomal RNA |   
8 | 5.8S ribosomal RNA |   
9 | 18S ribosomal RNA |   
A | uL2 | G1TT27_RABIT 1-257  
AA | uS2 |   
B | uL3 | G1TL06_RABIT 2-403  
BB | 40S ribosomal protein S3a | G1SS70_RABIT 1-264  
C | uL4 | G1SVW5_RABIT 1-378  
CC | uS5 |   
D | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297  
DD | uS4 | G1TNM3_RABIT 1-243  
E | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291  
EE | 40S ribosomal protein S4 |   
F | uL30 | G1TUB1_RABIT 1-247  
FF | Uncharacterized protein | G1TFM5_RABIT 1-204  
G | eL8 | G1STW0_RABIT 78-319  
GG | 40S ribosomal protein S6 | G1TM55_RABIT 1-249  
H | uL6 | G1TX33_RABIT 1-192  
HH | uS7 | G1SVB0_RABIT 1-194  
I | Ribosomal protein L10 (Predicted) | B7NZQ2_RABIT 1-214  
II | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208  
J | uL5 | G1TUB8_RABIT 1-178  
JJ | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194  
KK | eS10 | G1TPV3_RABIT 1-165  
L | eL13 |   
LL | uS17 | G1TRM4_RABIT 1-158  
M | eL14 | G1SZ12_RABIT 1-218  
MM | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132  
N | Ribosomal protein L15 | G1T0C1_RABIT 1-204  
NN | uS15 | G1SP51_RABIT 1-151  
O | uL13 |   
OO | uS11 | G1T1F0_RABIT -4-151  
P | uL22 | G1TVT6_RABIT 1-184  
PP | uS19 | G1U0Q2_RABIT 1-145  
Q | eL18 |   
QQ | uS9 | G1SGX4_RABIT 1-146  
R | eL19 |   
RR | eS17 | G1TU13_RABIT 1-135  
S | eL20 |   
SS | uS13 | G1TPG3_RABIT 1-152  
T | eL21 | G1SHQ2_RABIT 1-160  
TT | eS19 | G1TN62_RABIT 1-145  
U | eL22 |   
UU | uS10 | G1SIZ2_RABIT 1-119  
V | uL14 | G1T6D1_RABIT 1-140  
VV | eS21 |   
W | uL24 | G1SE28_RABIT 1-157  
WW | uS8 | G1TG89_RABIT 1-130  
X | uL23 | G1SE76_RABIT 1-156  
XX | uS12 |   
Y | uL24 | G1SQH0_RABIT 1-145  
YY | eS24 |   
Z | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136  
ZZ | eS25 | G1TDB3_RABIT 1-125  
a | uL15 | G1SNY0_RABIT 1-148  
aa | eS26 |   
b | eL29 | G1SGR6_RABIT 1-226  
bb | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84  
c | eL30 | G1TDL2_RABIT 1-115  
cc | eS28 | G1TIB4_RABIT 1-69  
d | eL31 | G1SHG0_RABIT 1-125  
dd | uS14 | G1U7M4_RABIT 1-56  
e | eL32 | G1U437_RABIT 1-135  
ee | eS30 | G1T8A2_RABIT 0-132  
f | eL33 | G1SF08_RABIT 1-110  
ff | eS31 | G1SK22_RABIT 1-156  
g | eL34 | G1U945_RABIT 1-116  
gg | RACK1 | G1SJB4_RABIT 1-317  
h | uL29 | G1SIT5_RABIT 1-123  
hh | mRNA |   
i | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105  
j | Ribosomal protein L37 | U3KPD5_RABIT 1-97  
jj | Elongation factor 1-alpha 1 | EF1A1_RABIT 1-462  
k | eL38 |   
l | eL39 | G1TTN1_RABIT 1-51  
m | eL40 |   
n | 60s ribosomal protein l41 |   
o | eL42 | G1U344_RABIT 1-106  
p | eL43 | G1SY53_RABIT 1-92  
r | eL28 | G1U7L1_RABIT 1-137  
s | uL10 |   
t | uL11 | G1SMR7_RABIT 1-165  
  

> select subtract /3

219341 atoms, 235173 bonds, 5821 pseudobonds, 18111 residues, 4 models
selected  

> color zone #4 near sel distance 24

[Repeated 1 time(s)]

> show #!59 models

> select add #59

427092 atoms, 458280 bonds, 10249 pseudobonds, 35175 residues, 7 models
selected  

> select subtract /PT

425448 atoms, 456444 bonds, 10172 pseudobonds, 35098 residues, 7 models
selected  

> color zone #4 near sel distance 24

[Repeated 1 time(s)]

> select clear

> color #4 darkgrey models

No atoms selected for color zoning  

> undo

[Repeated 1 time(s)]

> color zone #4 near sel distance 24

> hide #!4 models

> show #!5 models

> hide #!6 models

> show #!4 models

> show #!3 models

> hide #!4 models

> hide #!5 models

> hide #!59 models

> select add #59

427092 atoms, 458280 bonds, 10249 pseudobonds, 35175 residues, 7 models
selected  

> select add #6

428685 atoms, 460059 bonds, 10315 pseudobonds, 35250 residues, 7 models
selected  

> hide #!3 models

> select subtract #6

207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models
selected  

> select subtract #59

Nothing selected  

> show #!7 models

> show #!6 models

> show #!5 models

> hide #!6 models

> show #!50 models

> hide #!50 models

> color #5 #929292ff models

> select add #7/BT:139

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

> select add #7/eI:145

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select up

131 atoms, 130 bonds, 21 residues, 1 model selected  

> select up

2193 atoms, 2207 bonds, 364 residues, 1 model selected  

> show #!58 models

> color #5 darkgrey models

> hide #!5 models

> show #!61 models

> hide #!61 models

> show #!59 models

> hide #!59 models

> show #!60 models

> hide #!60 models

> show #!6 models

> hide #!6 models

> hide #!7 models

> show #!7 models

> select add #7

204962 atoms, 220182 bonds, 5230 pseudobonds, 16898 residues, 4 models
selected  

> show sel cartoons

> select #7/m:45

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1611 atoms, 1799 bonds, 76 residues, 1 model selected  

> select up

204962 atoms, 220182 bonds, 16898 residues, 1 model selected  

> color sel red

> undo

> select #7/m:45

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1611 atoms, 1799 bonds, 76 residues, 1 model selected  

> color sel red

> select add #7/eI:39

1617 atoms, 1804 bonds, 77 residues, 1 model selected  

> select add #7/BT:138

1622 atoms, 1808 bonds, 78 residues, 1 model selected  

> select up

1763 atoms, 1950 bonds, 100 residues, 1 model selected  

> select up

3804 atoms, 4006 bonds, 440 residues, 1 model selected  

> select ~sel & ##selected

201158 atoms, 216176 bonds, 5162 pseudobonds, 16458 residues, 4 models
selected  

> hide sel cartoons

> select ~sel & ##selected

3804 atoms, 4006 bonds, 68 pseudobonds, 440 residues, 2 models selected  

> select add #58

212940 atoms, 228725 bonds, 4581 pseudobonds, 17522 residues, 5 models
selected  

> show #!5 models

> color zone #5 near sel distance 24

> select #7/m:45

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1611 atoms, 1799 bonds, 76 residues, 1 model selected  

> select up

204962 atoms, 220182 bonds, 16898 residues, 1 model selected  

> select down

1611 atoms, 1799 bonds, 76 residues, 1 model selected  

> color sel orange red

> hide #!5 models

Drag select of 17522 residues, 11 pseudobonds  

> show #!5 models

> color zone #5 near sel distance 24

> hide #!7 models

> hide #!58 models

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/subunit_colouring.cxs
> includeMaps true

——— End of log from Tue Sep 24 13:28:01 2024 ———

opened ChimeraX session  

> show #!2 models

> hide #!2 models

> close #1,3-5

> show #!2 models

> hide #!2 models

> rename #2 ID #51

Expected a keyword  

> rename #2 id #51

> rename #6 id #52

> rename #7 id #53

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/160_APE_T8/1/MultiPostProcessor_PPout_1.mrc

Opened MultiPostProcessor_PPout_1.mrc as #1, grid size 128,128,128, pixel 4,
shown at level 0.814, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/160_APE_T8/2/MultiPostProcessor_PPout_2.mrc

Opened MultiPostProcessor_PPout_2.mrc as #2, grid size 128,128,128, pixel 4,
shown at level 0.879, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/160_APE_T8/3/MultiPostProcessor_PPout_3.mrc

Opened MultiPostProcessor_PPout_3.mrc as #3, grid size 128,128,128, pixel 4,
shown at level 0.948, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/160_APE_T8/4/MultiPostProcessor_PPout_4.mrc

Opened MultiPostProcessor_PPout_4.mrc as #4, grid size 128,128,128, pixel 4,
shown at level 0.794, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/160_APE_T8/5/MultiPostProcessor_PPout_5.mrc

Opened MultiPostProcessor_PPout_5.mrc as #5, grid size 128,128,128, pixel 4,
shown at level 0.914, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/160_APE_T8/6/MultiPostProcessor_PPout_6.mrc

Opened MultiPostProcessor_PPout_6.mrc as #6, grid size 128,128,128, pixel 4,
shown at level 0.951, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/160_APE_T8/7/MultiPostProcessor_PPout_7.mrc

Opened MultiPostProcessor_PPout_7.mrc as #7, grid size 128,128,128, pixel 4,
shown at level 0.831, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/160_APE_T8/8/MultiPostProcessor_PPout_8.mrc

Opened MultiPostProcessor_PPout_8.mrc as #8, grid size 128,128,128, pixel 4,
shown at level 0.868, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/160_APE_T8/9/MultiPostProcessor_PPout_9.mrc

Opened MultiPostProcessor_PPout_9.mrc as #9, grid size 128,128,128, pixel 4,
shown at level 0.845, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/160_APE_T8/10/MultiPostProcessor_PPout_10.mrc

Opened MultiPostProcessor_PPout_10.mrc as #10, grid size 128,128,128, pixel 4,
shown at level 0.911, step 1, values float32  

> select up

414098 atoms, 444901 bonds, 11 pseudobonds, 33980 residues, 3 models selected  

> select up

414098 atoms, 444901 bonds, 4513 pseudobonds, 33980 residues, 4 models
selected  

> select up

414098 atoms, 444901 bonds, 4513 pseudobonds, 33980 residues, 4 models
selected  

> select up

1477583 atoms, 1585013 bonds, 4513 pseudobonds, 122647 residues, 31 models
selected  

> select up

1477583 atoms, 1585013 bonds, 4513 pseudobonds, 122647 residues, 31 models
selected  

> select up

1477583 atoms, 1585013 bonds, 4513 pseudobonds, 122647 residues, 31 models
selected  

> select up

1477583 atoms, 1585013 bonds, 4513 pseudobonds, 122647 residues, 31 models
selected  

> select up

1477583 atoms, 1585013 bonds, 4513 pseudobonds, 122647 residues, 31 models
selected  

> select up

1477583 atoms, 1585013 bonds, 4513 pseudobonds, 122647 residues, 31 models
selected  

> select up

1477583 atoms, 1585013 bonds, 4513 pseudobonds, 122647 residues, 31 models
selected  

> volume #1-49 level 0.6

> select clear

> fitmap #1-49 inMap #50 eachModel true

Fit map MultiPostProcessor_PPout_1.mrc in map Stable_60S.mrc using 61817
points  
correlation = 0.7951, correlation about mean = 0.2961, overlap = 2.624e+04  
steps = 112, shift = 2.98, angle = 0.818 degrees  
  
Position of MultiPostProcessor_PPout_1.mrc (#1) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99999478 -0.00311186 0.00087074 -0.14379447  
0.00312366 0.99989855 -0.01389700 1.47273619  
-0.00082740 0.01389965 0.99990305 -5.78123811  
Axis 0.97402137 0.05950434 0.21849854  
Axis point 0.00000000 396.00399632 108.71750420  
Rotation angle (degrees) 0.81758223  
Shift along axis -1.31561680  
  
Fit map MultiPostProcessor_PPout_2.mrc in map Stable_60S.mrc using 61494
points  
correlation = 0.7972, correlation about mean = 0.3714, overlap = 2.908e+04  
steps = 64, shift = 0.644, angle = 0.506 degrees  
  
Position of MultiPostProcessor_PPout_2.mrc (#2) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99996222 0.00819146 0.00290805 -2.97912285  
-0.00818683 0.99996521 -0.00160000 2.16480691  
-0.00292106 0.00157613 0.99999449 -0.18911667  
Axis 0.17972266 0.32984235 -0.92677062  
Axis point 248.58380136 372.59760019 0.00000000  
Rotation angle (degrees) 0.50628434  
Shift along axis 0.35389688  
  
Fit map MultiPostProcessor_PPout_3.mrc in map Stable_60S.mrc using 65267
points  
correlation = 0.7898, correlation about mean = 0.3761, overlap = 3.186e+04  
steps = 88, shift = 0.243, angle = 0.7 degrees  
  
Position of MultiPostProcessor_PPout_3.mrc (#3) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99995276 -0.00828852 -0.00507807 3.09149523  
0.00825064 0.99993832 -0.00743584 -0.18987311  
0.00513939 0.00739360 0.99995946 -3.15144080  
Axis 0.60649564 -0.41787482 0.67641975  
Axis point 34.88087020 385.76547138 0.00000000  
Rotation angle (degrees) 0.70048778  
Shift along axis -0.17737525  
  
Fit map MultiPostProcessor_PPout_4.mrc in map Stable_60S.mrc using 59877
points  
correlation = 0.8022, correlation about mean = 0.3078, overlap = 2.557e+04  
steps = 88, shift = 2.34, angle = 0.278 degrees  
  
Position of MultiPostProcessor_PPout_4.mrc (#4) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99999430 -0.00050675 0.00333951 -1.63531040  
0.00051839 0.99999380 -0.00348431 0.47759630  
-0.00333772 0.00348603 0.99998835 -2.16532846  
Axis 0.71808864 0.68789181 0.10561046  
Axis point 0.00000000 589.75777236 348.14276568  
Rotation angle (degrees) 0.27808029  
Shift along axis -1.07444458  
  
Fit map MultiPostProcessor_PPout_5.mrc in map Stable_60S.mrc using 59232
points  
correlation = 0.7949, correlation about mean = 0.3447, overlap = 2.973e+04  
steps = 84, shift = 0.774, angle = 0.648 degrees  
  
Position of MultiPostProcessor_PPout_5.mrc (#5) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99996317 -0.00455944 0.00727169 -0.49148603  
0.00450574 0.99996259 0.00738415 -2.31152776  
-0.00730509 -0.00735111 0.99994630 3.19487684  
Axis -0.65134764 0.64434199 0.40071144  
Axis point 0.00000000 426.19068196 324.87901058  
Rotation angle (degrees) 0.64810733  
Shift along axis 0.11093758  
  
Fit map MultiPostProcessor_PPout_6.mrc in map Stable_60S.mrc using 63888
points  
correlation = 0.7961, correlation about mean = 0.385, overlap = 3.227e+04  
steps = 84, shift = 0.259, angle = 0.371 degrees  
  
Position of MultiPostProcessor_PPout_6.mrc (#6) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99997996 -0.00591460 -0.00225561 1.84682685  
0.00591152 0.99998159 -0.00137194 -0.95106575  
0.00226368 0.00135858 0.99999652 -1.01216912  
Axis 0.21082917 -0.34894394 0.91312058  
Axis point 173.85950933 318.89584750 0.00000000  
Rotation angle (degrees) 0.37103057  
Shift along axis -0.20299885  
  
Fit map MultiPostProcessor_PPout_7.mrc in map Stable_60S.mrc using 63186
points  
correlation = 0.808, correlation about mean = 0.3509, overlap = 2.777e+04  
steps = 88, shift = 1.94, angle = 0.176 degrees  
  
Position of MultiPostProcessor_PPout_7.mrc (#7) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99999794 -0.00202123 0.00018305 -0.59615874  
0.00202165 0.99999530 -0.00230642 0.56671006  
-0.00017839 0.00230679 0.99999732 -2.07649320  
Axis 0.75076350 0.05882043 0.65794705  
Axis point 0.00000000 392.67578006 290.31562031  
Rotation angle (degrees) 0.17603280  
Shift along axis -1.78046267  
  
Fit map MultiPostProcessor_PPout_8.mrc in map Stable_60S.mrc using 60436
points  
correlation = 0.8012, correlation about mean = 0.3659, overlap = 2.864e+04  
steps = 140, shift = 0.632, angle = 0.803 degrees  
  
Position of MultiPostProcessor_PPout_8.mrc (#8) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99995071 -0.00669777 -0.00732934 2.95979137  
0.00662503 0.99992900 -0.00990496 0.67021516  
0.00739516 0.00985591 0.99992408 -4.53011907  
Axis 0.70538554 -0.52560712 0.47557166  
Axis point 0.00000000 439.74884406 42.28488422  
Rotation angle (degrees) 0.80257623  
Shift along axis -0.41887207  
  
Fit map MultiPostProcessor_PPout_9.mrc in map Stable_60S.mrc using 64511
points  
correlation = 0.796, correlation about mean = 0.3277, overlap = 2.82e+04  
steps = 96, shift = 1.34, angle = 0.311 degrees  
  
Position of MultiPostProcessor_PPout_9.mrc (#9) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99998542 -0.00512424 -0.00170508 0.92464670  
0.00512514 0.99998673 0.00052400 -0.86445166  
0.00170237 -0.00053273 0.99999841 -1.27460130  
Axis -0.09737134 -0.31397800 0.94442397  
Axis point 231.71726915 160.35872034 0.00000000  
Rotation angle (degrees) 0.31090356  
Shift along axis -1.02237931  
  
Fit map MultiPostProcessor_PPout_10.mrc in map Stable_60S.mrc using 59509
points  
correlation = 0.7961, correlation about mean = 0.352, overlap = 2.962e+04  
steps = 100, shift = 0.624, angle = 0.833 degrees  
  
Position of MultiPostProcessor_PPout_10.mrc (#10) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99989435 0.01320815 0.00606920 -4.70713974  
-0.01320831 0.99991277 -0.00001366 2.88902403  
-0.00606885 -0.00006650 0.99998158 1.02994226  
Axis -0.00181751 0.41752076 -0.90866557  
Axis point 207.54686844 358.00321712 0.00000000  
Rotation angle (degrees) 0.83287245  
Shift along axis 0.27890971  
  

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> select add #51/w3:148

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

> select add #51/51:4034

30 atoms, 31 bonds, 2 residues, 1 model selected  

> select up

77872 atoms, 87115 bonds, 3641 residues, 1 model selected  

> select up

79568 atoms, 88840 bonds, 3852 residues, 1 model selected  

> show #!52 models

> select add #52

300502 atoms, 325792 bonds, 5887 pseudobonds, 22038 residues, 5 models
selected  

> select subtract #52

79568 atoms, 88840 bonds, 3852 residues, 1 model selected  

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> select #52/2:46

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> select up

220934 atoms, 236952 bonds, 18186 residues, 1 model selected  

> select down

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> select #52/ii:14

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

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1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> select up

220934 atoms, 236952 bonds, 18186 residues, 1 model selected  

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> select #52/ii:46

23 atoms, 25 bonds, 1 residue, 1 model selected  

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1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> color sel red

> select #52/2:15

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> color sel orange

> select #52/3:62

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

> select up

1593 atoms, 1779 bonds, 75 residues, 1 model selected  

> color sel yellow

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> show #!51 models

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> log metadata #52

No models had metadata

> log chains #52

Chain information for 5lzs #52  
---  
Chain | Description | UniProt  
2 ii | tRNA |   
3 | E-site tRNA |   
5 | 28S ribosomal RNA |   
7 | 5S ribosomal RNA |   
8 | 5.8S ribosomal RNA |   
9 | 18S ribosomal RNA |   
A | uL2 | G1TT27_RABIT 1-257  
AA | uS2 |   
B | uL3 | G1TL06_RABIT 2-403  
BB | 40S ribosomal protein S3a | G1SS70_RABIT 1-264  
C | uL4 | G1SVW5_RABIT 1-378  
CC | uS5 |   
D | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297  
DD | uS4 | G1TNM3_RABIT 1-243  
E | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291  
EE | 40S ribosomal protein S4 |   
F | uL30 | G1TUB1_RABIT 1-247  
FF | Uncharacterized protein | G1TFM5_RABIT 1-204  
G | eL8 | G1STW0_RABIT 78-319  
GG | 40S ribosomal protein S6 | G1TM55_RABIT 1-249  
H | uL6 | G1TX33_RABIT 1-192  
HH | uS7 | G1SVB0_RABIT 1-194  
I | Ribosomal protein L10 (Predicted) | B7NZQ2_RABIT 1-214  
II | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208  
J | uL5 | G1TUB8_RABIT 1-178  
JJ | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194  
KK | eS10 | G1TPV3_RABIT 1-165  
L | eL13 |   
LL | uS17 | G1TRM4_RABIT 1-158  
M | eL14 | G1SZ12_RABIT 1-218  
MM | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132  
N | Ribosomal protein L15 | G1T0C1_RABIT 1-204  
NN | uS15 | G1SP51_RABIT 1-151  
O | uL13 |   
OO | uS11 | G1T1F0_RABIT -4-151  
P | uL22 | G1TVT6_RABIT 1-184  
PP | uS19 | G1U0Q2_RABIT 1-145  
Q | eL18 |   
QQ | uS9 | G1SGX4_RABIT 1-146  
R | eL19 |   
RR | eS17 | G1TU13_RABIT 1-135  
S | eL20 |   
SS | uS13 | G1TPG3_RABIT 1-152  
T | eL21 | G1SHQ2_RABIT 1-160  
TT | eS19 | G1TN62_RABIT 1-145  
U | eL22 |   
UU | uS10 | G1SIZ2_RABIT 1-119  
V | uL14 | G1T6D1_RABIT 1-140  
VV | eS21 |   
W | uL24 | G1SE28_RABIT 1-157  
WW | uS8 | G1TG89_RABIT 1-130  
X | uL23 | G1SE76_RABIT 1-156  
XX | uS12 |   
Y | uL24 | G1SQH0_RABIT 1-145  
YY | eS24 |   
Z | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136  
ZZ | eS25 | G1TDB3_RABIT 1-125  
a | uL15 | G1SNY0_RABIT 1-148  
aa | eS26 |   
b | eL29 | G1SGR6_RABIT 1-226  
bb | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84  
c | eL30 | G1TDL2_RABIT 1-115  
cc | eS28 | G1TIB4_RABIT 1-69  
d | eL31 | G1SHG0_RABIT 1-125  
dd | uS14 | G1U7M4_RABIT 1-56  
e | eL32 | G1U437_RABIT 1-135  
ee | eS30 | G1T8A2_RABIT 0-132  
f | eL33 | G1SF08_RABIT 1-110  
ff | eS31 | G1SK22_RABIT 1-156  
g | eL34 | G1U945_RABIT 1-116  
gg | RACK1 | G1SJB4_RABIT 1-317  
h | uL29 | G1SIT5_RABIT 1-123  
hh | mRNA |   
i | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105  
j | Ribosomal protein L37 | U3KPD5_RABIT 1-97  
jj | Elongation factor 1-alpha 1 | EF1A1_RABIT 1-462  
k | eL38 |   
l | eL39 | G1TTN1_RABIT 1-51  
m | eL40 |   
n | 60s ribosomal protein l41 |   
o | eL42 | G1U344_RABIT 1-106  
p | eL43 | G1SY53_RABIT 1-92  
r | eL28 | G1U7L1_RABIT 1-137  
s | uL10 |   
t | uL11 | G1SMR7_RABIT 1-165  
  

> log metadata #52

No models had metadata

> log chains #52

Chain information for 5lzs #52  
---  
Chain | Description | UniProt  
2 ii | tRNA |   
3 | E-site tRNA |   
5 | 28S ribosomal RNA |   
7 | 5S ribosomal RNA |   
8 | 5.8S ribosomal RNA |   
9 | 18S ribosomal RNA |   
A | uL2 | G1TT27_RABIT 1-257  
AA | uS2 |   
B | uL3 | G1TL06_RABIT 2-403  
BB | 40S ribosomal protein S3a | G1SS70_RABIT 1-264  
C | uL4 | G1SVW5_RABIT 1-378  
CC | uS5 |   
D | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297  
DD | uS4 | G1TNM3_RABIT 1-243  
E | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291  
EE | 40S ribosomal protein S4 |   
F | uL30 | G1TUB1_RABIT 1-247  
FF | Uncharacterized protein | G1TFM5_RABIT 1-204  
G | eL8 | G1STW0_RABIT 78-319  
GG | 40S ribosomal protein S6 | G1TM55_RABIT 1-249  
H | uL6 | G1TX33_RABIT 1-192  
HH | uS7 | G1SVB0_RABIT 1-194  
I | Ribosomal protein L10 (Predicted) | B7NZQ2_RABIT 1-214  
II | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208  
J | uL5 | G1TUB8_RABIT 1-178  
JJ | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194  
KK | eS10 | G1TPV3_RABIT 1-165  
L | eL13 |   
LL | uS17 | G1TRM4_RABIT 1-158  
M | eL14 | G1SZ12_RABIT 1-218  
MM | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132  
N | Ribosomal protein L15 | G1T0C1_RABIT 1-204  
NN | uS15 | G1SP51_RABIT 1-151  
O | uL13 |   
OO | uS11 | G1T1F0_RABIT -4-151  
P | uL22 | G1TVT6_RABIT 1-184  
PP | uS19 | G1U0Q2_RABIT 1-145  
Q | eL18 |   
QQ | uS9 | G1SGX4_RABIT 1-146  
R | eL19 |   
RR | eS17 | G1TU13_RABIT 1-135  
S | eL20 |   
SS | uS13 | G1TPG3_RABIT 1-152  
T | eL21 | G1SHQ2_RABIT 1-160  
TT | eS19 | G1TN62_RABIT 1-145  
U | eL22 |   
UU | uS10 | G1SIZ2_RABIT 1-119  
V | uL14 | G1T6D1_RABIT 1-140  
VV | eS21 |   
W | uL24 | G1SE28_RABIT 1-157  
WW | uS8 | G1TG89_RABIT 1-130  
X | uL23 | G1SE76_RABIT 1-156  
XX | uS12 |   
Y | uL24 | G1SQH0_RABIT 1-145  
YY | eS24 |   
Z | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136  
ZZ | eS25 | G1TDB3_RABIT 1-125  
a | uL15 | G1SNY0_RABIT 1-148  
aa | eS26 |   
b | eL29 | G1SGR6_RABIT 1-226  
bb | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84  
c | eL30 | G1TDL2_RABIT 1-115  
cc | eS28 | G1TIB4_RABIT 1-69  
d | eL31 | G1SHG0_RABIT 1-125  
dd | uS14 | G1U7M4_RABIT 1-56  
e | eL32 | G1U437_RABIT 1-135  
ee | eS30 | G1T8A2_RABIT 0-132  
f | eL33 | G1SF08_RABIT 1-110  
ff | eS31 | G1SK22_RABIT 1-156  
g | eL34 | G1U945_RABIT 1-116  
gg | RACK1 | G1SJB4_RABIT 1-317  
h | uL29 | G1SIT5_RABIT 1-123  
hh | mRNA |   
i | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105  
j | Ribosomal protein L37 | U3KPD5_RABIT 1-97  
jj | Elongation factor 1-alpha 1 | EF1A1_RABIT 1-462  
k | eL38 |   
l | eL39 | G1TTN1_RABIT 1-51  
m | eL40 |   
n | 60s ribosomal protein l41 |   
o | eL42 | G1U344_RABIT 1-106  
p | eL43 | G1SY53_RABIT 1-92  
r | eL28 | G1U7L1_RABIT 1-137  
s | uL10 |   
t | uL11 | G1SMR7_RABIT 1-165  
  

> show #!52 target m

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> show #!52 target m

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> select add #52

220934 atoms, 236952 bonds, 5887 pseudobonds, 18186 residues, 4 models
selected  

> select subtract #52

Nothing selected  

> show #!51 models

> log metadata #51

No models had metadata

> log chains #51

Chain information for 6hcj #51  
---  
Chain | Description | UniProt  
1 | nascent chain |   
33 | P/E tRNA |   
51 | 28S ribosomal RNA |   
71 | 5S ribosomal RNA |   
81 | 5.8S ribosomal RNA |   
A2 | 18S ribosomal RNA |   
A3 | Ribosomal protein L8 | G1TT27_RABIT 1-257  
B2 | uS2 |   
B3 | uL3 | G1TL06_RABIT 2-403  
C2 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264  
C3 | uL4 |   
D2 | uS5 |   
D3 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297  
E2 | uS3 | G1TNM3_RABIT 1-243  
E3 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291  
F2 | eS4 |   
F3 | uL30 | G1TUB1_RABIT 1-247  
G2 | Ribosomal protein S5 | G1TFM5_RABIT 1-204  
G3 | eL8 |   
H2 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249  
H3 | uL6 | G1TX33_RABIT 1-192  
I2 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194  
I3 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214  
J2 | eS8 |   
J3 | Ribosomal protein L11 | G1TUB8_RABIT 1-178  
K2 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194  
L2 | eS10 | G1TPV3_RABIT 1-165  
L3 | eL13 |   
M2 | Ribosomal protein S11 | G1TRM4_RABIT 1-158  
M3 | Ribosomal protein L14 | G1SZ12_RABIT 1-218  
N2 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132  
N3 | Ribosomal protein L15 | G1T0C1_RABIT 1-204  
O2 | uS15 | G1SP51_RABIT 1-151  
O3 | uL13 |   
P2 | uS11 |   
P3 | uL22 | G1TVT6_RABIT 1-184  
Q2 | uS19 | G1U0Q2_RABIT 1-145  
Q3 | eL18 |   
R2 | Ribosomal protein S16 | G1SGX4_RABIT 1-146  
R3 | eL19 |   
S2 | eS17 | G1TU13_RABIT 1-135  
S3 | eL20 |   
T2 | uS13 | G1TPG3_RABIT 1-152  
T3 | eL21 | G1SHQ2_RABIT 1-160  
U2 | eS19 |   
U3 | eL22 |   
V2 | uS10 | G1SIZ2_RABIT 1-119  
V3 | Ribosomal protein L23 | G1T6D1_RABIT 1-140  
W2 | eS21 |   
X2 | Ribosomal protein S15a | G1TG89_RABIT 1-130  
X3 | uL23 | G1SE76_RABIT 1-156  
Y2 | uS12 |   
Y3 | Ribosomal protein L26 | G1SQH0_RABIT 1-145  
Z2 | eS24 |   
Z3 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136  
a2 | eS25 | G1TDB3_RABIT 1-125  
a3 | uL15 | G1SNY0_RABIT 2-148  
b2 | eS26 |   
b3 | eL29 | G1SGR6_RABIT 1-226  
c2 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84  
c3 | eL30 | G1TDL2_RABIT 1-115  
d2 | Ribosomal protein S28 | G1TIB4_RABIT 1-69  
d3 | eL31 | G1SHG0_RABIT 1-125  
e2 | uS14 | G1U7M4_RABIT 1-56  
e3 | eL32 | G1U437_RABIT 1-135  
f2 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132  
f3 | eL33 | G1SF08_RABIT 1-110  
g2 | Ribosomal protein S27a | G1SK22_RABIT 1-156  
g3 | eL34 |   
h2 | RACK1 | G1SJB4_RABIT 1-317  
h3 | uL29 | G1SIT5_RABIT 1-123  
i3 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105  
j3 | Ribosomal protein L37 | U3KPD5_RABIT 1-97  
k3 | eL38 |   
l3 | eL39 | G1TTN1_RABIT 1-51  
m3 | eL40 |   
n3 | eL41 |   
o3 | eL42 |   
p3 | eL43 | G1SY53_RABIT 1-92  
q3 | A/P RNA |   
r3 | eL28 | G1U7L1_RABIT 1-137  
t3 | uL10 |   
u3 | Ribosomal protein L12 | G1SMR7_RABIT 1-165  
v3 | mRNA |   
w3 | uL1 | G1SKZ8_RABIT 1-217  
  

> log metadata #51

No models had metadata

> log chains #51

Chain information for 6hcj #51  
---  
Chain | Description | UniProt  
1 | nascent chain |   
33 | P/E tRNA |   
51 | 28S ribosomal RNA |   
71 | 5S ribosomal RNA |   
81 | 5.8S ribosomal RNA |   
A2 | 18S ribosomal RNA |   
A3 | Ribosomal protein L8 | G1TT27_RABIT 1-257  
B2 | uS2 |   
B3 | uL3 | G1TL06_RABIT 2-403  
C2 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264  
C3 | uL4 |   
D2 | uS5 |   
D3 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297  
E2 | uS3 | G1TNM3_RABIT 1-243  
E3 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291  
F2 | eS4 |   
F3 | uL30 | G1TUB1_RABIT 1-247  
G2 | Ribosomal protein S5 | G1TFM5_RABIT 1-204  
G3 | eL8 |   
H2 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249  
H3 | uL6 | G1TX33_RABIT 1-192  
I2 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194  
I3 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214  
J2 | eS8 |   
J3 | Ribosomal protein L11 | G1TUB8_RABIT 1-178  
K2 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194  
L2 | eS10 | G1TPV3_RABIT 1-165  
L3 | eL13 |   
M2 | Ribosomal protein S11 | G1TRM4_RABIT 1-158  
M3 | Ribosomal protein L14 | G1SZ12_RABIT 1-218  
N2 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132  
N3 | Ribosomal protein L15 | G1T0C1_RABIT 1-204  
O2 | uS15 | G1SP51_RABIT 1-151  
O3 | uL13 |   
P2 | uS11 |   
P3 | uL22 | G1TVT6_RABIT 1-184  
Q2 | uS19 | G1U0Q2_RABIT 1-145  
Q3 | eL18 |   
R2 | Ribosomal protein S16 | G1SGX4_RABIT 1-146  
R3 | eL19 |   
S2 | eS17 | G1TU13_RABIT 1-135  
S3 | eL20 |   
T2 | uS13 | G1TPG3_RABIT 1-152  
T3 | eL21 | G1SHQ2_RABIT 1-160  
U2 | eS19 |   
U3 | eL22 |   
V2 | uS10 | G1SIZ2_RABIT 1-119  
V3 | Ribosomal protein L23 | G1T6D1_RABIT 1-140  
W2 | eS21 |   
X2 | Ribosomal protein S15a | G1TG89_RABIT 1-130  
X3 | uL23 | G1SE76_RABIT 1-156  
Y2 | uS12 |   
Y3 | Ribosomal protein L26 | G1SQH0_RABIT 1-145  
Z2 | eS24 |   
Z3 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136  
a2 | eS25 | G1TDB3_RABIT 1-125  
a3 | uL15 | G1SNY0_RABIT 2-148  
b2 | eS26 |   
b3 | eL29 | G1SGR6_RABIT 1-226  
c2 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84  
c3 | eL30 | G1TDL2_RABIT 1-115  
d2 | Ribosomal protein S28 | G1TIB4_RABIT 1-69  
d3 | eL31 | G1SHG0_RABIT 1-125  
e2 | uS14 | G1U7M4_RABIT 1-56  
e3 | eL32 | G1U437_RABIT 1-135  
f2 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132  
f3 | eL33 | G1SF08_RABIT 1-110  
g2 | Ribosomal protein S27a | G1SK22_RABIT 1-156  
g3 | eL34 |   
h2 | RACK1 | G1SJB4_RABIT 1-317  
h3 | uL29 | G1SIT5_RABIT 1-123  
i3 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105  
j3 | Ribosomal protein L37 | U3KPD5_RABIT 1-97  
k3 | eL38 |   
l3 | eL39 | G1TTN1_RABIT 1-51  
m3 | eL40 |   
n3 | eL41 |   
o3 | eL42 |   
p3 | eL43 | G1SY53_RABIT 1-92  
q3 | A/P RNA |   
r3 | eL28 | G1U7L1_RABIT 1-137  
t3 | uL10 |   
u3 | Ribosomal protein L12 | G1SMR7_RABIT 1-165  
v3 | mRNA |   
w3 | uL1 | G1SKZ8_RABIT 1-217  
  

> select #51/q3:46

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1579 atoms, 1765 bonds, 74 residues, 1 model selected  

> color sel orange red

> select #51/33:44

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1604 atoms, 1795 bonds, 75 residues, 1 model selected  

> color sel yellow

> select clear

Drag select of 18 residues  

> hide #!51 models

> show #!52 models

> show #!51 models

> hide #!51 models

> hide #!52 models

> select clear

> show #!53 models

> select #53/m:21

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

> select down

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

> select up

1611 atoms, 1799 bonds, 76 residues, 1 model selected  

> select up

204962 atoms, 220182 bonds, 16898 residues, 1 model selected  

> select down

1611 atoms, 1799 bonds, 76 residues, 1 model selected  

> select down

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

> select up

1611 atoms, 1799 bonds, 76 residues, 1 model selected  

> color sel red

> hide #!53 models

> show #!58 models

> select #58/PT:51

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

> select up

1644 atoms, 1836 bonds, 77 residues, 1 model selected  

> color sel yellow

> show #!51 models

> hide #!51 models

> show #!51 models

> show #!52 models

> hide #!51 models

> color sel orange

> show #!53 models

> hide #!53 models

> show #!53 models

> hide #!58 models

> hide #!53 models

> hide #!52 models

> show #!59 models

> show #!60 models

> hide #!59 models

> hide #!60 models

> show #!61 models

> hide #!61 models

> show #!51 models

> show #!52 models

> show #!53 models

> show #!61 models

> hide #!61 models

> show #!58 models

> hide #!58 models

> show #!58 models

> hide #!58 models

> show #!58 models

> hide #!58 models

> select #51/q3:14

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

> select up

1579 atoms, 1765 bonds, 74 residues, 1 model selected  

> color sel orange

> hide #!51 models

> hide #!52 models

> show #!52 models

> hide #!53 models

> show #!58 models

> select add #52/2:46

1602 atoms, 1790 bonds, 75 residues, 2 models selected  

> select #58/PT:47

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #52/2:46

46 atoms, 50 bonds, 2 residues, 2 models selected  

> select up

3260 atoms, 3642 bonds, 153 residues, 2 models selected  

> color sel light sea green

> color sel magenta

> color sel gray

> color sel yellow

> show #!53 models

> hide #!53 models

> show #!51 models

> hide #!51 models

> show #!51 models

> select add #51/33:50

3280 atoms, 3663 bonds, 154 residues, 3 models selected  

> select #51/33:49

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

> select up

1604 atoms, 1795 bonds, 75 residues, 1 model selected  

> color sel cyan

> color sel light sea green

> color sel lime

> show #!53 models

> show #!59 models

> show #!60 models

> show #!61 models

> hide #!52 models

> hide #!53 models

> hide #!58 models

> hide #!59 models

> hide #!61 models

> show #!52 models

> hide #!51 models

> hide #!52 models

> select clear

> show #!52 models

> show #!53 models

> hide #!53 models

> hide #!52 models

> show #!59 models

> hide #!59 models

> show #!58 models

> hide #!58 models

> show #!53 models

> hide #!53 models

> show #!52 models

> show #!51 models

> hide #!52 models

> hide #!51 models

> show #!51 models

> hide #!51 models

> show #!58 models

> show #!59 models

> hide #!60 models

> show #!61 models

> hide #!59 models

> hide #!58 models

> select #61/18S:1549

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

> hide #!61 models

> show #!59 models

> select #59/1S:1550

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

> hide #!59 models

> show #!58 models

> select #58/1S:1562

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide #!58 models

> show #!53 models

> hide #!53 models

> show #!52 models

> show #!61 models

> select #52/9:1613

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide #!52 models

> select #61/18S:1208

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

> hide #!61 models

> show #!59 models

> select add #59/1S:1237

45 atoms, 49 bonds, 2 residues, 2 models selected  

> hide #!59 models

> show #!58 models

> select add #58/15:32

53 atoms, 56 bonds, 3 residues, 3 models selected  

> hide #!58 models

> show #!53 models

> hide #!53 models

> show #!52 models

> select add #52/9:1614

75 atoms, 80 bonds, 4 residues, 4 models selected  

> hide #!52 models

> show #!51 models

> select add #51/A2:1618

95 atoms, 101 bonds, 5 residues, 5 models selected  

> select up

148307 atoms, 165843 bonds, 6959 residues, 5 models selected  

> select up

149228 atoms, 166785 bonds, 7074 residues, 5 models selected  

> select up

149495 atoms, 166785 bonds, 7341 residues, 5 models selected  

> select up

1064570 atoms, 1142269 bonds, 87881 residues, 5 models selected  

> select down

149495 atoms, 166785 bonds, 7341 residues, 5 models selected  

> select up

1064570 atoms, 1142269 bonds, 87881 residues, 5 models selected  

> select down

149495 atoms, 166785 bonds, 7341 residues, 5 models selected  

> select ssu

362373 atoms, 396658 bonds, 12006 pseudobonds, 23927 residues, 14 models
selected  

> show #!58 models

> hide #!58 models

> hide #!51 models

> show #!51 models

> hide #!51 models

> show #!51 models

> show #!52 models

> hide #!52 models

> hide #!51 models

> show #!52 models

> show #!51 models

> hide #!52 models

> hide #!51 models

> show #!60 models

> color (#!60 & sel) dark gray

> show #!59 models

> hide #!60 models

> show #!60 models

> hide #!59 models

> show #!59 models

> show #!61 models

> show #!58 models

> color (#!58-61 & sel) black

> hide #!60 models

> select add #60

465371 atoms, 502150 bonds, 12484 pseudobonds, 36459 residues, 14 models
selected  

> select subtract #60

257320 atoms, 279588 bonds, 7349 pseudobonds, 18591 residues, 10 models
selected  

> select down

262618 atoms, 285926 bonds, 7349 pseudobonds, 18427 residues, 12 models
selected  

> select clear

> select ssu

362373 atoms, 396658 bonds, 12006 pseudobonds, 23927 residues, 14 models
selected  

> select add #60

465371 atoms, 502150 bonds, 12484 pseudobonds, 36459 residues, 14 models
selected  

> select subtract #60

257320 atoms, 279588 bonds, 7349 pseudobonds, 18591 residues, 10 models
selected  

> hide #!61 models

> show #!61 models

> hide #!59 models

> hide #!61 models

> hide #!58 models

> show #!59 models

> hide #!59 models

> show #!61 models

> hide #!61 models

> show #!59 models

> show #!58 models

> color (#!58-59 & sel) dim gray

> show #!61 models

> hide #!61 models

> select add #61

359396 atoms, 384312 bonds, 7876 pseudobonds, 30861 residues, 10 models
selected  

> select subtract #61

152330 atoms, 162598 bonds, 2807 pseudobonds, 13258 residues, 6 models
selected  

> select ~sel & ##selected

264557 atoms, 285228 bonds, 6134 pseudobonds, 20888 residues, 6 models
selected  

> select subtract #58/PT

262913 atoms, 283392 bonds, 6053 pseudobonds, 20811 residues, 6 models
selected  

> color (#!58-59 & sel) light sea green

> hide #!58 models

> hide #!59 models

> select clear

> show #!51 models

> show #!52 models

> hide #!52 models

> show #!58 models

> hide #!51 models

> rename #58 "Unrotated, P"

> hide #!58 models

> show #!59 models

> rename #58 "Unrotated base, P"

> rename #59 "Rotated base"

> show #!53 models

> hide #!59 models

> show #!58 models

> hide #!58 models

> select #53/BT:179

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

> select up

95 atoms, 94 bonds, 19 residues, 1 model selected  

> select up

1050 atoms, 1049 bonds, 210 residues, 1 model selected  

> color sel light sea green

> rename #53 A

> show #!58 models

> hide #!58 models

> rename #53 "A, IF5 and L-contact"

> hide #!53 models

> show #!52 models

> rename #52 "EF1, A/T, P, E"

> hide #!52 models

> show #!51 models

> show #!59 models

> rename #51 "A/P, P/E"

> show #!60 models

> hide #!59 models

> hide #!51 models

> hide #!60 models

> show #!61 models

> select ssu

362373 atoms, 396658 bonds, 12006 pseudobonds, 23927 residues, 14 models
selected  

> select clear

> log metadata #61

No models had metadata

> log chains #61

Chain information for 7osm #61  
---  
Chain | Description | UniProt  
18S | 18S rRNA |   
25S | 25S rRNA |   
58S | 5.8S rRNA |   
AB | 5S rRNA |   
ASIT | PHE tRNA |   
PSIT | FMET tRNA |   
RACK | BJ4_G0022010.mRNA.1.CDS.1 | A0A6L1BKH8_YEASX 1-319  
eEF2 | Elongation factor 2 | A0A6A5Q7K2_YEASX 1-842  
eL13 | 60S ribosomal protein L13 | A0A6L1AF71_YEASX 1-199  
eL14 | 60S ribosomal protein L14-A | RL14A_YEAST 1-138  
eL15 | 60S ribosomal protein L15-A | RL15A_YEAST 1-204  
eL18 | BJ4_G0033900.mRNA.1.CDS.1 | A0A6L1A7F6_YEASX 1-186  
eL19 | 60S ribosomal protein L19-A | RL19A_YEAST 1-189  
eL20 | 60S ribosomal protein L20 | A0A6V8RR03_YEASX 1-172  
eL21 | BJ4_G0003770.mRNA.1.CDS.1 | A0A6L0YTI6_YEASX 1-160  
eL22 | 60S ribosomal protein L22-A | A0A6L0ZZW6_YEASX 1-121  
eL24 | 60S ribosomal protein L24-A | A0A6A5PY83_YEASX 1-155  
eL27 | 60S ribosomal protein L27 | A0A6L0ZQQ7_YEASX 1-136  
eL29 | 60S ribosomal protein L29 | A0A6A5PWR1_YEASX 1-59  
eL30 | BJ4_G0020000.mRNA.1.CDS.1 | A0A6L0ZM08_YEASX 1-105  
eL31 | BJ4_G0008090.mRNA.1.CDS.1 | A0A6L0YFR2_YEASX 1-113  
eL32 | HN1_G0013350.mRNA.1.CDS.1 | A0A7I9CD28_YEASX 1-130  
eL33 | BJ4_G0025510.mRNA.1.CDS.1 | A0A6L1C3H0_YEASX 1-107  
eL34 | 60S ribosomal protein L34-A | A0A6L0ZFW3_YEASX 1-121  
eL36 | 60S ribosomal protein L36-A | RL36A_YEAST 1-100  
eL37 | Ribosomal protein L37 | A0A6L1BIE7_YEASX 1-88  
eL38 | BJ4_G0032190.mRNA.1.CDS.1 | A0A6A5PUL8_YEASX 1-78  
eL39 | 60S ribosomal protein L39 | A0A6L1ASX0_YEASX 1-51  
eL40 | Ubiquitin | A0A6V8S9K0_YEASX 1-128  
eL41 | eL41 |   
eL42 | BJ4_G0001880.mRNA.1.CDS.1 | A0A6L1B5X0_YEASX 1-106  
eL43 | 60S ribosomal protein L43-A | RL43A_YEAST 1-92  
eL6 | 60S ribosomal protein L6 | A0A6L1BLT3_YEASX 1-176  
eL8 | 60S ribosomal protein L8-A | RL8A_YEAST 1-256  
eS1 | 40S ribosomal protein S1 | A0A6A5PRY4_YEASX 1-255  
eS10 | 40S ribosomal protein S10-A | A0A6L0ZM59_YEASX 1-105  
eS17 | BJ4_G0020710.mRNA.1.CDS.1 | A0A6L1BLL7_YEASX 1-136  
eS19 | 40S ribosomal protein S19-A | A0A6L1BWT3_YEASX 1-144  
eS21 | 40S ribosomal protein S21 | A0A6L1BDN3_YEASX 1-87  
eS24 | 40S ribosomal protein S24 | A0A6L1AUB6_YEASX 1-135  
eS25 | 40S ribosomal protein S25 | A0A6A5PZ18_YEASX 1-108  
eS26 | 40S ribosomal protein S26 | A0A6A5PUG0_YEASX 1-119  
eS27 | 40S ribosomal protein S27-A | RS27A_YEAST 1-82  
eS28 | eS28 | A0A6A5Q700_YEASX 1-67  
eS30 | 40S ribosomal protein S30 | A0A6L1A1E1_YEASX 1-63  
eS31 | Ubiquitin-40S ribosomal protein S31 | A0A6A5PU37_YEASX 1-152  
eS4 | 40S ribosomal protein S4 | A0A6L0Z3Q0_YEASX 1-261  
eS6 | 40S ribosomal protein S6 | A0A6L1AMY1_YEASX 1-236  
eS7 | 40S ribosomal protein S7 | A0A6L1ACT7_YEASX 1-190  
eS8 | 40S ribosomal protein S8 | A0A6A5Q1H1_YEASX 1-200  
mRNA | MRNA |   
uL10 | 60S acidic ribosomal protein P0 | A0A6A5PT43_YEASX 1-312  
uL11 | 60S ribosomal protein L12-B | A0A6A5Q275_YEASX 1-165  
uL13 | 60S ribosomal protein L16-A | A0A6L0ZD57_YEASX 1-199  
uL14 | 60S ribosomal protein L23-B | A0A6L0Z7E4_YEASX 1-137  
uL15 | 60S ribosomal protein L28 | A0A6L0ZDK5_YEASX 1-149  
uL16 | 60S ribosomal protein L10 | A0A6A5PUZ5_YEASX 1-221  
uL18 | 60S ribosomal protein L5 | A0A6A5Q0W8_YEASX 1-297  
uL2 | 60S ribosomal protein L2-B | A0A6L0Y8L2_YEASX 1-254  
uL22 | BJ4_G0005750.mRNA.1.CDS.1 | A0A6L1BCL1_YEASX 1-184  
uL23 | 60S ribosomal protein L25 | A0A6L0YSM0_YEASX 1-142  
uL24 | 60S ribosomal protein L26-A | RL26A_YEAST 1-127  
uL29 | BJ4_G0044250.mRNA.1.CDS.1 | A0A7I9BRN0_YEASX 1-120  
uL3 | 60S ribosomal protein L3 | A0A6A5Q627_YEASX 1-387  
uL30 | 60S ribosomal protein L7-A | A0A6V8RJA7_YEASX 1-244  
uL4 | BJ4_G0008850.mRNA.1.CDS.1 | A0A6A5Q3W0_YEASX 1-362  
uL5 | BJ4_G0027750.mRNA.1.CDS.1 | A0A6A5Q7I9_YEASX 1-174  
uL6 | 60S ribosomal protein L9-A | RL9A_YEAST 1-191  
uS10 | 40S ribosomal protein S20 | A0A6A5PVE9_YEASX 1-121  
uS11 | 40S ribosomal protein S14-A | A0A6L1AAG7_YEASX 1-137  
uS12 | 40S ribosomal protein S23 | A0A6L1B1T2_YEASX 1-145  
uS13 | 40S ribosomal protein S18-B | A0A6L1AIT6_YEASX 1-146  
uS14 | HLJ1_G0030400.mRNA.1.CDS.1 | A0A6A5PV92_YEASX 1-56  
uS15 | 40S ribosomal protein S13 | A0A6L0YFM5_YEASX 1-151  
uS17 | 40S ribosomal protein S11-B | A0A6L0YMX6_YEASX 1-156  
uS19 | 40S ribosomal protein S15 | A0A6A5Q6F2_YEASX 1-142  
uS2 | 40S ribosomal protein S0 | A0A6L0ZRP4_YEASX 1-252  
uS3 | BJ4_G0045400.mRNA.1.CDS.1 | A0A6L0ZVK6_YEASX 1-240  
uS4 | BJ4_G0026100.mRNA.1.CDS.1 | A0A7I9GPQ3_YEASX 1-197  
uS5 | 40S ribosomal protein S2 | A0A6A5PWF7_YEASX 1-254  
uS7 | Rps5p | A0A1L4AA68_YEASX 1-225  
uS8 | 40S ribosomal protein S22-A | A0A6A5PSE9_YEASX 1-130  
uS9 | BJ4_G0008010.mRNA.1.CDS.1 | A0A6L0YQ58_YEASX 1-143  
  

> select /uS*

34320 atoms, 34900 bonds, 17 pseudobonds, 4395 residues, 6 models selected  

> select /eS*

33073 atoms, 33567 bonds, 21 pseudobonds, 4183 residues, 6 models selected  

> select add /uS*

67393 atoms, 68467 bonds, 38 pseudobonds, 8578 residues, 6 models selected  

> select ~sel & ##selected

347724 atoms, 375809 bonds, 10166 pseudobonds, 26893 residues, 8 models
selected  

> select add /mRNA

347724 atoms, 375809 bonds, 10166 pseudobonds, 26893 residues, 8 models
selected  

> select /eS*

33073 atoms, 33567 bonds, 21 pseudobonds, 4183 residues, 6 models selected  

> select add /uS*

67393 atoms, 68467 bonds, 38 pseudobonds, 8578 residues, 6 models selected  

> select add /mRNA

67628 atoms, 68727 bonds, 38 pseudobonds, 8590 residues, 6 models selected  

> select add /18S

141363 atoms, 150942 bonds, 3028 pseudobonds, 12268 residues, 8 models
selected  

> select add /5S

146523 atoms, 156710 bonds, 3246 pseudobonds, 12510 residues, 12 models
selected  

> select add /58S

153245 atoms, 164202 bonds, 3413 pseudobonds, 12842 residues, 12 models
selected  

> select subtract /58S

146523 atoms, 156710 bonds, 3246 pseudobonds, 12510 residues, 12 models
selected  

> select add /rRACK

146523 atoms, 156710 bonds, 3246 pseudobonds, 12510 residues, 12 models
selected  

> select add /RACK

151395 atoms, 161688 bonds, 3246 pseudobonds, 13146 residues, 12 models
selected  

> color (#!61 & sel) dim gray

> show #!59 models

> hide #!61 models

> hide #!59 models

> show #!61 models

> show #!59 models

> hide #!61 models

> select add #58

357951 atoms, 383523 bonds, 7652 pseudobonds, 30107 residues, 13 models
selected  

> select subtract #58

148815 atoms, 158804 bonds, 3139 pseudobonds, 13025 residues, 10 models
selected  

> select add #59

353986 atoms, 379027 bonds, 7456 pseudobonds, 29968 residues, 11 models
selected  

> select subtract #59

146235 atoms, 155920 bonds, 3028 pseudobonds, 12904 residues, 8 models
selected  

> select add #60

280135 atoms, 299484 bonds, 6634 pseudobonds, 24175 residues, 8 models
selected  

> select subtract #60

72084 atoms, 76922 bonds, 1499 pseudobonds, 6307 residues, 4 models selected  

> show #!60 models

> hide #!60 models

> show #!61 models

> show #!58 models

> hide #!58 models

> select ~sel & ##selected

134982 atoms, 144792 bonds, 3567 pseudobonds, 11296 residues, 4 models
selected  

> hide #!59 models

> select subtract /eEF2

128375 atoms, 138063 bonds, 3558 pseudobonds, 10447 residues, 4 models
selected  

> color (#!61 & sel) light sea green

> select clear

> hide #!61 models

> show #!61 models

> rename #61 "Swivel base, eEF2"

> show #!51 models

> hide #!51 models

> show #!60 models

> hide #!61 models

> show #!51 models

> show #!61 models

> hide #!61 models

> show #!61 models

> hide #!60 models

> show #!60 models

> hide #!60 models

> show #!52 models

> hide #!52 models

> show #!53 models

> hide #!53 models

> hide #!51 models

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/subunit_colouring2.cxs
> includeMaps true

> show #!2 models

> hide #!61 models

> show #!52 models

> hide #!2 models

> select #52/jj:436

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

> select add #52/ii:49

24 atoms, 24 bonds, 2 residues, 1 model selected  

> select add #52/2:9

46 atoms, 48 bonds, 3 residues, 1 model selected  

> select add #52/jj:402

53 atoms, 54 bonds, 4 residues, 1 model selected  

> select #52/jj:401

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

> select add #52/ii:13

28 atoms, 28 bonds, 2 residues, 1 model selected  

> select add #52/2:13

48 atoms, 49 bonds, 3 residues, 1 model selected  

> select add #52/3:7

70 atoms, 73 bonds, 4 residues, 1 model selected  

> select up

4888 atoms, 5454 bonds, 236 residues, 1 model selected  

> select up

8208 atoms, 8844 bonds, 668 residues, 1 model selected  

> select ~sel & ##selected

212726 atoms, 228108 bonds, 5690 pseudobonds, 17518 residues, 4 models
selected  

> hide

> hide sel

> hide #!52 models

> show #!52 models

> hide sel cartoons

> hide #!52 models

> show #!53 models

> hide #!53 models

> show #!52 models

> show #!51 models

> hide #!52 models

> hide #!51 models

> show #!52 models

> show #!3 models

> hide #!3 models

> show #!2 models

> show #!58 models

> hide #!52 models

> show #!52 models

> hide #!2 models

> hide #!52 models

> show #!52 models

> hide #!52 models

> select #58/ET:52

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

> select up

1644 atoms, 1836 bonds, 77 residues, 1 model selected  

> hide sel cartoons

> show #!52 models

> select add #52

222578 atoms, 238788 bonds, 5887 pseudobonds, 18263 residues, 5 models
selected  

> select add #58

430070 atoms, 461671 bonds, 10400 pseudobonds, 35268 residues, 7 models
selected  

> show #!2 models

> ui tool show "Color Zone"

> color zone #2 near sel distance 12

> color single #2

> hide #!2 models

> select subtract #58

220934 atoms, 236952 bonds, 5887 pseudobonds, 18186 residues, 4 models
selected  

> select add #58

430070 atoms, 461671 bonds, 10400 pseudobonds, 35268 residues, 7 models
selected  

> select subtract #58

220934 atoms, 236952 bonds, 5887 pseudobonds, 18186 residues, 4 models
selected  

> select subtract #52

Nothing selected  

> hide #!58 models

Drag select of 668 residues  

> show #!58 models

Drag select of 17673 residues, 11 pseudobonds  

> show #!2 models

> color zone #2 near sel distance 12

> hide #!52 models

> hide #!58 models

> color zone #2 near sel distance 15

> color #2 black models

[Repeated 1 time(s)]

> color #2 #fac8ffff models

> color #2 #fff5fbff models

> color #2 #fffffbff models

> color #2 white models

> color zone #2 near sel distance 15

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!2 models

> volume #2 level 0.6072

> volume #2 level 0.6

> hide #!2 models

> show #!3 models

> volume #3 level 0.65

> show #!2 models

> hide #!2 models

> select clear

> show #!61 models

> hide #!3 models

> show #!52 models

> hide #!52 models

> select clear

> select #61/ASIT:45

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

> select add #61/PSIT:13

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select up

3280 atoms, 3663 bonds, 153 residues, 1 model selected  

> hide sel cartoons

> show #!52 models

> select #52/3:52

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1593 atoms, 1779 bonds, 75 residues, 1 model selected  

> hide #!52 models

Drag select of 16942 residues, 28 pseudobonds  

> show #!3 models

> color #3 #ffffb2ff models

> color #3 white models

> color zone #2 near sel distance 15

> show #!2 models

> hide #!2 models

> show #!2 models

[Repeated 1 time(s)]

> hide #!3 models

> undo

[Repeated 1 time(s)]

> show #!2 models

> hide #!2 models

> undo

[Repeated 5 time(s)]

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!3 models

> color zone #3 near sel distance 15

> hide #!61 models

> volume #3 level 0.7

> show #!58 models

> show #!61 models

> hide #!58 models

> show #!58 models

> select add #58/L1:133

204849 atoms, 1787 bonds, 28 pseudobonds, 17018 residues, 4 models selected  

> hide #!3 models

> hide #!58 models

> show #!58 models

> hide #!58 models

> show #!58 models

> hide #!61 models

> select add #58/2S:2481

204872 atoms, 1812 bonds, 28 pseudobonds, 17019 residues, 4 models selected  

> select up

276418 atoms, 81796 bonds, 28 pseudobonds, 20441 residues, 4 models selected  

> hide #!58 models

> show #!3 models

> color zone #3 near sel distance 15

> show #!58 models

> select add #58/31:117

276426 atoms, 81803 bonds, 28 pseudobonds, 20442 residues, 4 models selected  

> select up

276536 atoms, 81915 bonds, 28 pseudobonds, 20457 residues, 4 models selected  

> select up

277563 atoms, 82956 bonds, 28 pseudobonds, 20594 residues, 4 models selected  

> select up

278095 atoms, 301007 bonds, 28 pseudobonds, 21095 residues, 4 models selected  

> select up

637136 atoms, 683385 bonds, 28 pseudobonds, 52871 residues, 4 models selected  

> select down

278095 atoms, 301007 bonds, 28 pseudobonds, 21095 residues, 4 models selected  

> select up

637136 atoms, 683385 bonds, 28 pseudobonds, 52871 residues, 4 models selected  

> select down

278095 atoms, 301007 bonds, 28 pseudobonds, 21095 residues, 4 models selected  

> select add #58/20:99

278103 atoms, 301014 bonds, 28 pseudobonds, 21096 residues, 4 models selected  

> select up

278154 atoms, 301065 bonds, 28 pseudobonds, 21102 residues, 4 models selected  

> select up

278951 atoms, 301873 bonds, 28 pseudobonds, 21202 residues, 4 models selected  

> color zone #3 near sel distance 15

> hide #!58 models

> hide #!3 models

> show #!4 models

> color #4 #ffffb2ff models

> color #4 white models

> show #!58 models

> hide #!4 models

Drag select of 17005 residues, 11 pseudobonds  
[Repeated 1 time(s)]

> show #!4 models

> color zone #3 near sel distance 15

> hide #!4 models

> show #!3 models

[Repeated 1 time(s)]

> hide #!3 models

> color zone #4 near sel distance 24

> color zone #4 near sel distance 15

[Repeated 1 time(s)]

> volume #4 level 0.5353

> hide #!58 models

> show #!3 models

> show #!2 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!3 models

> show #!53 models

> hide #!53 models

> show #!61 models

> hide #!61 models

> show #!59 models

> hide #!59 models

> show #!53 models

> hide #!53 models

Drag select of 3 MultiPostProcessor_PPout_3.mrc  

> select clear

Drag select of 3 MultiPostProcessor_PPout_3.mrc  

> select clear

> show #!4 models

> hide #!3 models

> hide #!4 models

> show #!5 models

> color #5 #ffbf99ff models

> color #5 #ffff99ff models

> color #5 white models

> show #!58 models

> show #!53 models

> hide #!5 models

Drag select of 17445 residues, 11 pseudobonds  

> color zone #5 near sel distance 24

> show #!5 models

> hide #!53 models

> hide #!58 models

> show #!53 models

> select #53/eI:145

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

> select up

71 atoms, 71 bonds, 9 residues, 1 model selected  

> select up

1143 atoms, 1158 bonds, 154 residues, 1 model selected  

> color sel purple

> show #!52 models

> hide #!52 models

> color zone #5 near sel distance 24

> show #!58 models

Drag select of 17445 residues, 11 pseudobonds, 5
MultiPostProcessor_PPout_5.mrc  

> color zone #5 near sel distance 24

> hide #!5 models

> show #!6 models

> hide #!53 models

> hide #!58 models

> color #6 #ffbfe5ff models

> color #6 #ffffe5ff models

> color #6 white models

> show #!61 models

> hide #!6 models

> hide #!61 models

> show #!58 models

> show #!53 models

> hide #!58 models

Drag select of 362 residues  
Drag select of 364 residues  

> select add #61

209259 atoms, 221714 bonds, 5069 pseudobonds, 17967 residues, 5 models
selected  

> color zone #6 near sel distance 24

> show #!6 models

> hide #!6 models

> show #!8 models

> color #8 #ffb2b2ff models

> color #8 #ffffb2ff models

> color #8 white models

> show #!51 models

> hide #!53 models

> select clear

> hide #!8 models

> select #51/q3:46

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #51/33:14

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select up

3183 atoms, 3560 bonds, 149 residues, 1 model selected  

> show #!59 models

> hide #!51 models

Drag select of 17064 residues, 12 pseudobonds  

> color zone #8 near sel distance 24

> show #!8 models

> select subtract /PT

209290 atoms, 3560 bonds, 12 pseudobonds, 17136 residues, 3 models selected  

> color zone #8 near sel distance 24

> hide #!59 models

> show #!61 models

> select add #61/eEF2:724

209298 atoms, 3567 bonds, 12 pseudobonds, 17137 residues, 4 models selected  

> select up

209404 atoms, 3676 bonds, 12 pseudobonds, 17150 residues, 4 models selected  

> select up

215859 atoms, 10255 bonds, 12 pseudobonds, 17978 residues, 4 models selected  

> color zone #8 near sel distance 24

> hide #!61 models

> hide #!8 models

> show #!10 models

> color #10 white models

> select clear

> show #!52 models

> hide #!10 models

Drag select of 668 residues  

> select #52/jj:142

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

> select add #52/ii:51

27 atoms, 27 bonds, 2 residues, 1 model selected  

> select add #52/2:20

47 atoms, 48 bonds, 3 residues, 1 model selected  

> select up

3335 atoms, 3716 bonds, 165 residues, 1 model selected  

> select up

6615 atoms, 7065 bonds, 593 residues, 1 model selected  

> show #!58 models

> hide #!52 models

Drag select of 17005 residues, 11 pseudobonds  

> hide #!58 models

> show #!53 models

Drag select of 364 residues  

> show #!10 models

> color zone #10 near sel distance 24

> hide #!53 models

> show #!8 models

> show #!6 models

> show #!5 models

> show #!4 models

> show #!3 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!6 models

> hide #!8 models

> hide #!10 models

> hide #!5 models

> show #!2 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!6 models

> hide #!6 models

> show #!6 models

> show #!2 models

> hide #!6 models

> show #!10 models

> hide #!10 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> show #!2 models

> hide #!4 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> volume #5 level 0.6765

> show #!2 models

> hide #!5 models

> select up

216408 atoms, 7177 bonds, 11 pseudobonds, 17965 residues, 4 models selected  

> select up

635032 atoms, 681853 bonds, 11 pseudobonds, 52166 residues, 4 models selected  

> select up

635032 atoms, 681853 bonds, 4513 pseudobonds, 52166 residues, 5 models
selected  

> select up

635032 atoms, 681853 bonds, 4513 pseudobonds, 52166 residues, 5 models
selected  

> select up

1477583 atoms, 1585013 bonds, 4513 pseudobonds, 122647 residues, 25 models
selected  

> select clear

> volume #1-10 level 0.7

> volume #1-10 level 0.77

> volume #1-10 level 0.7

> volume #2 level 0.65

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> volume #4 level 0.6

> hide #!4 models

> show #!5 models

> volume #4 level 0.55

> show #!4 models

> hide #!5 models

> show #!3 models

> hide #!4 models

> show #!2 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> hide #!2 models

> show #!4 models

> show #!5 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!5 models

> show #!5 models

> hide #!2 models

> volume #5 level 0.65

> show #!6 models

> hide #!5 models

> hide #!6 models

> show #!8 models

> volume #8 level 0.6

> hide #!8 models

> show #!10 models

> volume #10 level 0.65

> volume #10 level 0.66

> volume #10 level 0.6

> volume #10 level 0.65

> hide #!10 models

> show #!8 models

> show #!10 models

> hide #!10 models

> hide #!8 models

> show #!6 models

> hide #!6 models

> show #!8 models

> hide #!8 models

> show #!10 models

> hide #!10 models

> show #!6 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> volume #2 level 0.66

> volume #2 level 0.6

> show #!4 models

> hide #!2 models

> volume #4 level 0.5

> volume #4 level 0.55

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!8 models

> hide #!8 models

> show #!10 models

> hide #!10 models

> show #!4 models

> show #!3 models

> hide #!4 models

> show #!5 models

> hide #!3 models

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/Class3D/job270/run_it025_class001.mrc

Opened run_it025_class001.mrc as #1, grid size 128,128,128, pixel 4, shown at
level 0.272, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/Class3D/job270/run_it025_class002.mrc

Opened run_it025_class002.mrc as #7, grid size 128,128,128, pixel 4, shown at
level 0.257, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/Class3D/job270/run_it025_class003.mrc

Opened run_it025_class003.mrc as #9, grid size 128,128,128, pixel 4, shown at
level 0.241, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/Class3D/job270/run_it025_class004.mrc

Opened run_it025_class004.mrc as #11, grid size 128,128,128, pixel 4, shown at
level 0.274, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/Class3D/job270/run_it025_class005.mrc

Opened run_it025_class005.mrc as #12, grid size 128,128,128, pixel 4, shown at
level 0.268, step 1, values float32  

> show #!4 models

> hide #!4 models

> hide #!5 models

> volume #1-10 level 0.7

> volume #1-10 level 0.6

> hide #!7 models

> hide #!9 models

> hide #!11 models

> hide #!12 models

> show #!58 models

> hide #!58 models

> show #!58 models

> hide #!58 models

> show #!59 models

> hide #!1 models

> show #!7 models

> volume #1-10 level 0.5

> hide #!7 models

> show #!9 models

> hide #!9 models

> show #!11 models

> volume #1-10 level 0.6

> volume #1-30 level 0.6

> hide #!11 models

> show #!12 models

> hide #!12 models

> hide #!59 models

> close #1,7,9,11-12

> rename #2 id #1

> rename #3 id #2

> rename #4 id #3

> rename #5 id #4

> rename #6 id #5

> rename #8 id #6

> rename #10 id #7

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> hide #!4 models

> hide #!6 models

> show #!6 models

> hide #!7 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!6 models

> show #!6 models

> hide #!1 models

> show #!58 models

> hide #!58 models

> show #!59 models

> select #59/PT:45

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

> select up

1644 atoms, 1836 bonds, 77 residues, 1 model selected  

> color sel cyan

> hide #!6 models

> color sel blue

> hide #!59 models

> show #!59 models

> hide #!59 models

> show #!59 models

> show #!6 models

> hide #!6 models

> show #!7 models

> show #!5 models

> hide #!7 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!59 models

> show #!58 models

> hide #!2 models

> show #!1 models

> hide #!58 models

> show #!58 models

> hide #!58 models

> show #!52 models

> show #!2 models

> hide #!1 models

> show #!59 models

> hide #!52 models

> show #!52 models

> hide #!52 models

> hide #!2 models

> color sel lime

> hide #!59 models

> show #!52 models

> select #52/3:52

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1593 atoms, 1779 bonds, 75 residues, 1 model selected  

> color sel blue

> color sel cornflower blue

> show #!1 models

> hide #!1 models

Drag select of 668 residues  

> show #!58 models

Drag select of 17673 residues, 11 pseudobonds  

> show #!1 models

> color zone #1 near sel distance 15

> hide #!1 models

> show #!2 models

> show #!61 models

> hide #!52 models

> hide #!58 models

> hide #!2 models

Drag select of 16942 residues, 28 pseudobonds  

> show #!2 models

> show #!52 models

> hide #!61 models

> show #!61 models

> hide #!2 models

> hide #!61 models

> show #!51 models

> show #!2 models

> show #!61 models

> hide #!61 models

> hide #!52 models

> show #!58 models

> hide #!58 models

> show #!61 models

> hide #!51 models

> hide #!2 models

> show #!2 models

> show #!59 models

> show #!58 models

> hide #!59 models

> hide #!58 models

> hide #!61 models

> show #!52 models

> show #!61 models

> hide #!61 models

> select add #52/3:53

203270 atoms, 25 bonds, 28 pseudobonds, 16943 residues, 3 models selected  

> select up

204840 atoms, 1779 bonds, 28 pseudobonds, 17017 residues, 3 models selected  

> color zone #2 near sel distance 15

> show #!58 models

> hide #!2 models

> hide #!52 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

Drag select of 17005 residues, 11 pseudobonds  

> select subtract /PT

410688 atoms, 1779 bonds, 39 pseudobonds, 33945 residues, 5 models selected  

> show #!2 models

> color zone #2 near sel distance 15

> hide #!58 models

> select clear

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> show #!3 models

> show #!7 models

> show #!6 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!6 models

> hide #!7 models

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/270_subclRot_from160_tRNAcleft_T6C5/1/MultiPostProcessor_PPout_1.mrc

Opened MultiPostProcessor_PPout_1.mrc as #8, grid size 128,128,128, pixel 4,
shown at level 0.863, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/270_subclRot_from160_tRNAcleft_T6C5/2/MultiPostProcessor_PPout_2.mrc

Opened MultiPostProcessor_PPout_2.mrc as #9, grid size 128,128,128, pixel 4,
shown at level 0.855, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/270_subclRot_from160_tRNAcleft_T6C5/3/MultiPostProcessor_PPout_3.mrc

Opened MultiPostProcessor_PPout_3.mrc as #10, grid size 128,128,128, pixel 4,
shown at level 0.899, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/270_subclRot_from160_tRNAcleft_T6C5/4/MultiPostProcessor_PPout_4.mrc

Opened MultiPostProcessor_PPout_4.mrc as #11, grid size 128,128,128, pixel 4,
shown at level 0.816, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/MultiPostProcessor/270_subclRot_from160_tRNAcleft_T6C5/5/MultiPostProcessor_PPout_5.mrc

Opened MultiPostProcessor_PPout_5.mrc as #12, grid size 128,128,128, pixel 4,
shown at level 0.868, step 1, values float32  

> volume #1-30 level 0.6

> hide #!9 models

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!8 models

> show #!9 models

> show #!52 models

> hide #!52 models

> show #!51 models

> hide #!9 models

> show #!10 models

> show #!11 models

> hide #!10 models

> show #!12 models

> hide #!11 models

> show #!52 models

> hide #!52 models

> show #!53 models

> hide #!53 models

> show #!53 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!12 models

> hide #!51 models

> hide #!53 models

> show #!9 models

> show #!11 models

> hide #!4 models

> hide #!11 models

> show #!8 models

> hide #!8 models

> hide #!9 models

> show #!9 models

> show #!10 models

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-HSCombine42C30C/Refine3D/job266/run_ct19_class001.mrc

Opened run_ct19_class001.mrc as #13, grid size 128,128,128, pixel 4, shown at
level 0.894, step 1, values float32  

> hide #!9 models

> hide #!10 models

> volume #1-30 level 0.6

> show #!52 models

> fitmap #1-40 inMap #50 eachModel true

Fit map MultiPostProcessor_PPout_2.mrc in map Stable_60S.mrc using 61494
points  
correlation = 0.7972, correlation about mean = 0.3714, overlap = 2.908e+04  
steps = 60, shift = 0.0149, angle = 0.0175 degrees  
  
Position of MultiPostProcessor_PPout_2.mrc (#1) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99996069 0.00834456 0.00299651 -3.02823774  
-0.00833904 0.99996352 -0.00184959 2.27584414  
-0.00301184 0.00182453 0.99999380 -0.22546558  
Axis 0.20288702 0.33178492 -0.92127934  
Axis point 257.42188875 372.58339778 0.00000000  
Rotation angle (degrees) 0.51879664  
Shift along axis 0.34841741  
  
Fit map MultiPostProcessor_PPout_3.mrc in map Stable_60S.mrc using 65267
points  
correlation = 0.7898, correlation about mean = 0.3762, overlap = 3.187e+04  
steps = 84, shift = 0.037, angle = 0.00881 degrees  
  
Position of MultiPostProcessor_PPout_3.mrc (#2) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99995216 -0.00830957 -0.00515952 3.11792540  
0.00827176 0.99993909 -0.00730734 -0.19952646  
0.00521993 0.00726431 0.99995999 -3.11566445  
Axis 0.59737632 -0.42551375 0.67976436  
Axis point 35.74099618 387.26843499 0.00000000  
Rotation angle (degrees) 0.69881820  
Shift along axis -0.17044159  
  
Fit map MultiPostProcessor_PPout_4.mrc in map Stable_60S.mrc using 59877
points  
correlation = 0.8022, correlation about mean = 0.3083, overlap = 2.557e+04  
steps = 80, shift = 0.0678, angle = 0.0206 degrees  
  
Position of MultiPostProcessor_PPout_4.mrc (#3) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99999347 -0.00056959 0.00356852 -1.62356182  
0.00058106 0.99999467 -0.00321407 0.37901028  
-0.00356667 0.00321613 0.99998847 -2.00390261  
Axis 0.66470224 0.73757905 0.11894566  
Axis point -528.06741878 0.00000000 260.65659024  
Rotation angle (degrees) 0.27713522  
Shift along axis -1.03799067  
  
Fit map MultiPostProcessor_PPout_5.mrc in map Stable_60S.mrc using 59232
points  
correlation = 0.7949, correlation about mean = 0.3444, overlap = 2.973e+04  
steps = 48, shift = 0.0725, angle = 0.0055 degrees  
  
Position of MultiPostProcessor_PPout_5.mrc (#4) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99996286 -0.00461161 0.00728096 -0.51123150  
0.00455843 0.99996293 0.00730449 -2.33296897  
-0.00731438 -0.00727103 0.99994681 3.11807221  
Axis -0.64569384 0.64657195 0.40623168  
Axis point 420.91878956 0.00000000 64.52893459  
Rotation angle (degrees) 0.64669460  
Shift along axis 0.08832642  
  
Fit map MultiPostProcessor_PPout_6.mrc in map Stable_60S.mrc using 63888
points  
correlation = 0.7961, correlation about mean = 0.3852, overlap = 3.228e+04  
steps = 136, shift = 0.044, angle = 0.0411 degrees  
  
Position of MultiPostProcessor_PPout_6.mrc (#5) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99998304 -0.00555169 -0.00175997 1.66698372  
0.00554863 0.99998309 -0.00174134 -0.79097248  
0.00176960 0.00173155 0.99999694 -1.00123439  
Axis 0.28572448 -0.29038792 0.91325592  
Axis point 154.40556504 310.51951823 0.00000000  
Rotation angle (degrees) 0.34820770  
Shift along axis -0.20839632  
  
Fit map MultiPostProcessor_PPout_8.mrc in map Stable_60S.mrc using 60436
points  
correlation = 0.8012, correlation about mean = 0.366, overlap = 2.864e+04  
steps = 116, shift = 0.00626, angle = 0.0226 degrees  
  
Position of MultiPostProcessor_PPout_8.mrc (#6) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99994835 -0.00684295 -0.00751427 3.03854961  
0.00677078 0.99993111 -0.00958843 0.55698488  
0.00757937 0.00953705 0.99992580 -4.49296038  
Axis 0.68526973 -0.54080825 0.48778256  
Axis point 0.00000000 450.35255951 31.69567556  
Rotation angle (degrees) 0.79957195  
Shift along axis -0.41058369  
  
Fit map MultiPostProcessor_PPout_10.mrc in map Stable_60S.mrc using 59509
points  
correlation = 0.7961, correlation about mean = 0.3516, overlap = 2.961e+04  
steps = 48, shift = 0.0691, angle = 0.0366 degrees  
  
Position of MultiPostProcessor_PPout_10.mrc (#7) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99988875 0.01353316 0.00627287 -4.81161824  
-0.01353012 0.99990832 -0.00052693 3.03578769  
-0.00627942 0.00044200 0.99998019 0.93789419  
Axis 0.03246164 0.42053636 -0.90669477  
Axis point 213.55266833 357.94621771 0.00000000  
Rotation angle (degrees) 0.85512209  
Shift along axis 0.27008234  
  
Fit map MultiPostProcessor_PPout_1.mrc in map Stable_60S.mrc using 66804
points  
correlation = 0.7951, correlation about mean = 0.3069, overlap = 2.904e+04  
steps = 76, shift = 1.93, angle = 0.932 degrees  
  
Position of MultiPostProcessor_PPout_1.mrc (#8) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99996069 -0.00883156 0.00078819 1.03071097  
0.00884149 0.99986787 -0.01364083 1.58158215  
-0.00066762 0.01364727 0.99990665 -4.78177885  
Axis 0.83850468 0.04473395 0.54305504  
Axis point 0.00000000 285.06991180 118.63299268  
Rotation angle (degrees) 0.93235131  
Shift along axis -1.66176272  
  
Fit map MultiPostProcessor_PPout_2.mrc in map Stable_60S.mrc using 62077
points  
correlation = 0.791, correlation about mean = 0.2657, overlap = 2.758e+04  
steps = 84, shift = 1.46, angle = 1.12 degrees  
  
Position of MultiPostProcessor_PPout_2.mrc (#9) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99991876 -0.00785846 -0.01003594 3.20150229  
0.00770891 0.99985996 -0.01485404 1.51864833  
0.01015126 0.01477546 0.99983931 -6.81126959  
Axis 0.75804480 -0.51647172 0.39827761  
Axis point 0.00000000 432.79952830 60.94586255  
Rotation angle (degrees) 1.11982388  
Shift along axis -1.07023292  
  
Fit map MultiPostProcessor_PPout_3.mrc in map Stable_60S.mrc using 60821
points  
correlation = 0.7944, correlation about mean = 0.3445, overlap = 2.933e+04  
steps = 64, shift = 0.608, angle = 1.13 degrees  
  
Position of MultiPostProcessor_PPout_3.mrc (#10) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99988940 -0.00885711 -0.01194710 4.62621771  
0.00870083 0.99987673 -0.01306975 0.87103265  
0.01206138 0.01296435 0.99984321 -6.17270861  
Axis 0.65862428 -0.60737904 0.44419001  
Axis point 0.00000000 469.08244460 51.81269293  
Rotation angle (degrees) 1.13246748  
Shift along axis -0.22396315  
  
Fit map MultiPostProcessor_PPout_4.mrc in map Stable_60S.mrc using 60145
points  
correlation = 0.7937, correlation about mean = 0.2541, overlap = 2.537e+04  
steps = 56, shift = 7.25, angle = 2.15 degrees  
  
Position of MultiPostProcessor_PPout_4.mrc (#11) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99987436 -0.00096549 0.01582179 -8.15441416  
0.00150250 0.99942192 -0.03396408 4.37484907  
-0.01577985 0.03398358 0.99929781 -8.54539822  
Axis 0.90623957 0.42148116 0.03291632  
Axis point 0.00000000 249.88026453 196.86866069  
Rotation angle (degrees) 2.14845329  
Shift along axis -5.82721939  
  
Fit map MultiPostProcessor_PPout_5.mrc in map Stable_60S.mrc using 66523
points  
correlation = 0.7747, correlation about mean = 0.2296, overlap = 2.812e+04  
steps = 76, shift = 1.49, angle = 0.784 degrees  
  
Position of MultiPostProcessor_PPout_5.mrc (#12) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99998582 -0.00480367 -0.00229697 0.86721561  
0.00477431 0.99990898 -0.01261903 2.07541331  
0.00235738 0.01260788 0.99991774 -4.82104454  
Axis 0.92128078 -0.16997565 0.34978565  
Axis point 0.00000000 348.92494991 145.24557039  
Rotation angle (degrees) 0.78447350  
Shift along axis -1.24015287  
  
Fit map run_ct19_class001.mrc in map Stable_60S.mrc using 64019 points  
correlation = 0.8011, correlation about mean = 0.358, overlap = 3.027e+04  
steps = 60, shift = 11.4, angle = 0.525 degrees  
  
Position of run_ct19_class001.mrc (#13) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.99996051 -0.00461062 0.00759751 -7.65443076  
0.00459392 0.99998700 0.00221376 -6.18437965  
-0.00760762 -0.00217877 0.99996869 -5.41230517  
Axis -0.23991258 0.83048002 0.50273740  
Axis point -318.49414300 0.00000000 1195.95239537  
Rotation angle (degrees) 0.52451734  
Shift along axis -6.02057771  
  

> hide #!52 models

> show #!51 models

> show #!58 models

> hide #!51 models

> show #!59 models

> hide #!58 models

> close #13

> hide #!59 models

> show #!1 models

> show #!8 models

> show #!9 models

> show #!10 models

> show #!11 models

> show #!12 models

> close #8-12

> hide #!1 models

> show #!1 models

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/160_decodingE.mrc
> models #1

[Repeated 1 time(s)]

> rename #1 160_decodingE.mrc

> hide #!1 models

> show #!2 models

> rename #2 170_hibernatingE.mrc

> hide #!2 models

> show #!3 models

> rename #3 160_Post?.mrc

> rename #2 160_hibernatingE.mrc

> hide #!3 models

> show #!4 models

> rename #4 160_unpre5.mrc

> hide #!4 models

> show #!5 models

> rename #5 160_hibernating5

> rename #4 160_unr_pre5.mrc

> hide #!5 models

> show #!6 models

> rename #6 160_rot

> hide #!6 models

> show #!7 models

> rename #7 160_decoding5

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/subunit_colouring2.cxs
> includeMaps true

——— End of log from Wed Jan 15 14:45:55 2025 ———

> view name session-start

opened ChimeraX session  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Combined_202505/MultiPostProcessor/Comb25_Subclass/Decoding2_IF5/MultiPostProcessor_PPout_Decoding2_IF5.mrc

Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc as #8, grid size
128,128,128, pixel 4, shown at level 0.93, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Combined_202505/MultiPostProcessor/Comb25_Subclass/Hibernating_IF5/MultiPostProcessor_PPout_Hibernating_IF5.mrc

Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc as #9, grid size
128,128,128, pixel 4, shown at level 0.945, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Combined_202505/MultiPostProcessor/Comb25_Subclass/Post_E/MultiPostProcessor_PPout_Post_E.mrc

Opened MultiPostProcessor_PPout_Post_E.mrc as #10, grid size 128,128,128,
pixel 4, shown at level 0.839, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Combined_202505/MultiPostProcessor/Comb25_Subclass/Rotated1/MultiPostProcessor_PPout_Rotated1.mrc

Opened MultiPostProcessor_PPout_Rotated1.mrc as #11, grid size 128,128,128,
pixel 4, shown at level 0.846, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Combined_202505/MultiPostProcessor/Comb25_Subclass/Rotated2/MultiPostProcessor_PPout_Rotated2.mrc

Opened MultiPostProcessor_PPout_Rotated2.mrc as #12, grid size 128,128,128,
pixel 4, shown at level 0.872, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Combined_202505/MultiPostProcessor/Comb25_Subclass/Translocating_E/MultiPostProcessor_PPout_Translocating_E.mrc

Opened MultiPostProcessor_PPout_Translocating_E.mrc as #13, grid size
128,128,128, pixel 4, shown at level 0.888, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Combined_202505/MultiPostProcessor/Comb25_Subclass/UnrotatedPre_cEF2_IF5/MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc

Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc as #14, grid size
128,128,128, pixel 4, shown at level 0.913, step 1, values float32  

> close #1-7

> volume #1-40 level 0.6

> fitmap #1-40 inMap #50 eachModel true

Fit map MultiPostProcessor_PPout_Decoding2_IF5.mrc in map Stable_60S.mrc using
59486 points  
correlation = 0.7898, correlation about mean = 0.3255, overlap = 2.952e+04  
steps = 64, shift = 1.68, angle = 1.28 degrees  
  
Position of MultiPostProcessor_PPout_Decoding2_IF5.mrc (#8) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99976397 0.01860026 0.01122686 -7.81996437  
-0.01865785 0.99981319 0.00504636 4.91861513  
-0.01113090 -0.00525464 0.99992424 3.63276708  
Axis -0.23067534 0.50066776 -0.83433847  
Axis point 226.38325290 407.97261497 0.00000000  
Rotation angle (degrees) 1.27940265  
Shift along axis 1.23550762  
  
Fit map MultiPostProcessor_PPout_Hibernating_IF5.mrc in map Stable_60S.mrc
using 63153 points  
correlation = 0.7951, correlation about mean = 0.3571, overlap = 3.106e+04  
steps = 56, shift = 2.13, angle = 0.404 degrees  
  
Position of MultiPostProcessor_PPout_Hibernating_IF5.mrc (#9) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99998335 0.00399359 0.00416445 -2.88996695  
-0.00401047 0.99998375 0.00405231 1.89960466  
-0.00414820 -0.00406894 0.99998312 1.76556607  
Axis -0.57552687 0.58909134 -0.56722149  
Axis point 667.29705654 0.00000000 450.51779174  
Rotation angle (degrees) 0.40425323  
Shift along axis 1.78082725  
  
Fit map MultiPostProcessor_PPout_Post_E.mrc in map Stable_60S.mrc using 60107
points  
correlation = 0.7977, correlation about mean = 0.318, overlap = 2.695e+04  
steps = 104, shift = 2, angle = 1.09 degrees  
  
Position of MultiPostProcessor_PPout_Post_E.mrc (#10) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99982744 0.01371127 0.01253378 -7.21702630  
-0.01375872 0.99989847 0.00370712 4.05104519  
-0.01248168 -0.00387893 0.99991458 3.11397695  
Axis -0.20005445 0.65969141 -0.72442078  
Axis point 201.53103384 501.74928587 0.00000000  
Rotation angle (degrees) 1.08639112  
Shift along axis 1.86040835  
  
Fit map MultiPostProcessor_PPout_Rotated1.mrc in map Stable_60S.mrc using
56561 points  
correlation = 0.8025, correlation about mean = 0.3245, overlap = 2.656e+04  
steps = 84, shift = 2.21, angle = 0.299 degrees  
  
Position of MultiPostProcessor_PPout_Rotated1.mrc (#11) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99999877 0.00066264 -0.00141870 -1.10491254  
-0.00066971 0.99998736 -0.00498347 3.14612435  
0.00141538 0.00498441 0.99998658 -1.97454050  
Axis 0.95402431 -0.27124992 -0.12751899  
Axis point 0.00000000 439.95627731 540.07575665  
Rotation angle (degrees) 0.29932172  
Shift along axis -1.65570799  
  
Fit map MultiPostProcessor_PPout_Rotated2.mrc in map Stable_60S.mrc using
55876 points  
correlation = 0.7965, correlation about mean = 0.3517, overlap = 2.697e+04  
steps = 52, shift = 2.02, angle = 0.557 degrees  
  
Position of MultiPostProcessor_PPout_Rotated2.mrc (#12) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99997820 0.00283253 -0.00596421 -0.55492718  
-0.00287500 0.99997049 -0.00712463 3.98347982  
0.00594385 0.00714162 0.99995683 -3.24244224  
Axis 0.73387023 -0.61256256 -0.29360107  
Axis point 0.00000000 534.32330989 393.93820254  
Rotation angle (degrees) 0.55691667  
Shift along axis -1.89539064  
  
Fit map MultiPostProcessor_PPout_Translocating_E.mrc in map Stable_60S.mrc
using 58868 points  
correlation = 0.7979, correlation about mean = 0.3674, overlap = 2.84e+04  
steps = 80, shift = 1.98, angle = 0.696 degrees  
  
Position of MultiPostProcessor_PPout_Translocating_E.mrc (#13) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99993288 0.01035511 0.00519701 -4.62869601  
-0.01037408 0.99993958 0.00363590 3.43941422  
-0.00515905 -0.00368957 0.99997989 1.98852097  
Axis -0.30142925 0.42613230 -0.85296640  
Axis point 281.27959097 414.91524566 0.00000000  
Rotation angle (degrees) 0.69623142  
Shift along axis 1.16472830  
  
Fit map MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc in map
Stable_60S.mrc using 58278 points  
correlation = 0.7868, correlation about mean = 0.3156, overlap = 2.842e+04  
steps = 64, shift = 2.56, angle = 0.963 degrees  
  
Position of MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc (#14) relative
to Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99992656 0.00215832 0.01192513 -4.02215773  
-0.00229700 0.99992976 0.01162790 0.14047040  
-0.01189920 -0.01165443 0.99986128 5.37646741  
Axis -0.69275610 0.70888307 -0.13256612  
Axis point 473.55149272 0.00000000 213.95372323  
Rotation angle (degrees) 0.96285115  
Shift along axis 2.17321395  
  

> hide #!9 models

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> show #!52 models

> show #!58 models

> hide #!8 models

> hide #!52 models

> show #!52 models

> hide #!52 models

> show #!52 models

Drag select of 17673 residues, 11 pseudobonds  

> select subtract #52/3

214107 atoms, 11 pseudobonds, 17598 residues, 3 models selected  

> ui tool show "Color Zone"

> show #!8 models

> show #!53 models

> hide #!58 models

> hide #!52 models

> hide #!8 models

Drag select of 364 residues  

> show #!52 models

> hide #!52 models

> show #!58 models

> show #!8 models

> color zone #50 near sel distance 24

> color zone #8 near sel distance 24

> hide #!53 models

> hide #!58 models

> hide #!8 models

> show #!9 models

> show #!8 models

> hide #!9 models

> surface dust #8 size 40

> hide #!8 models

> show #!9 models

> show #!61 models

> select clear

> hide #!9 models

> select add #61

207066 atoms, 221714 bonds, 5069 pseudobonds, 17603 residues, 4 models
selected  

> show sel cartoons

> undo

Drag select of 16942 residues, 28 pseudobonds  

> show #!51 models

> hide #!51 models

> show #!53 models

> hide #!61 models

Drag select of 364 residues  

> show #!61 models

> show #!9 models

> color zone #9 near sel distance 24

> select clear

> hide #!53 models

> hide #!61 models

> show #!61 models

> show #!53 models

> hide #!9 models

> hide #!53 models

Drag select of 16942 residues, 28 pseudobonds  

> show #!60 models

> hide #!60 models

> show #!53 models

> hide #!61 models

Drag select of 364 residues  

> color zone #9 near sel distance 30

[Repeated 1 time(s)]

> show #!9 models

> hide #!9 models

> show #!10 models

> hide #!53 models

> show #!58 models

> show #!51 models

> hide #!51 models

> show #!52 models

> select clear

> select add #58

209136 atoms, 224719 bonds, 4513 pseudobonds, 17082 residues, 3 models
selected  

> select add #52/3:44

209159 atoms, 224744 bonds, 4513 pseudobonds, 17083 residues, 4 models
selected  

> select up

210729 atoms, 226498 bonds, 4513 pseudobonds, 17157 residues, 4 models
selected  

> color zone #10 near sel distance 24

> hide #!58 models

> show #!58 models

> hide #!52 models

> show #!52 models

> hide #!58 models

> show #!58 models

> select subtract #58

1593 atoms, 1779 bonds, 75 residues, 1 model selected  

> hide #!52 models

> hide #!10 models

Drag select of 17005 residues, 11 pseudobonds  

> show #!52 models

> hide #!52 models

> show #!52 models

> hide #!58 models

> select add #52/3:52

207515 atoms, 25 bonds, 11 pseudobonds, 17006 residues, 3 models selected  

> select up

209085 atoms, 1779 bonds, 11 pseudobonds, 17080 residues, 3 models selected  

> select add #52/2:19

209108 atoms, 1804 bonds, 11 pseudobonds, 17081 residues, 3 models selected  

> select up

210701 atoms, 3585 bonds, 11 pseudobonds, 17156 residues, 3 models selected  

> show #!10 models

> color zone #10 near sel distance 24

> hide #!10 models

> show #!11 models

> hide #!52 models

> select clear

> show #!51 models

> hide #!11 models

> select #51/33:50

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

> select add #51/q3:20

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select up

3183 atoms, 3560 bonds, 149 residues, 1 model selected  

> show #!11 models

> hide #!11 models

> show #!59 models

> hide #!51 models

Drag select of 17064 residues, 12 pseudobonds  

> show #!51 models

> hide #!59 models

> select subtract #51/51

210934 atoms, 3560 bonds, 12 pseudobonds, 17213 residues, 3 models selected  

> select subtract #51/33

209330 atoms, 1765 bonds, 12 pseudobonds, 17138 residues, 3 models selected  

> show #!59 models

> hide #!51 models

> show #!10 models

> hide #!10 models

> show #!11 models

> show #!51 models

> color zone #10 near sel distance 24

> color zone #11 near sel distance 24

> hide #!11 models

> show #!12 models

> show #!61 models

> select add #61/eEF2:796

209338 atoms, 1772 bonds, 12 pseudobonds, 17139 residues, 4 models selected  

> select up

209421 atoms, 1861 bonds, 12 pseudobonds, 17148 residues, 4 models selected  

> select up

215899 atoms, 8460 bonds, 12 pseudobonds, 17980 residues, 4 models selected  

> color zone #12 near sel distance 24

> hide #!12 models

> show #!13 models

> hide #!59 models

> hide #!51 models

> hide #!13 models

> show #!13 models

> hide #!13 models

Drag select of 16942 residues, 28 pseudobonds  

> show #!52 models

> hide #!61 models

Drag select of 146 residues  

> select up

206456 atoms, 3585 bonds, 28 pseudobonds, 17093 residues, 3 models selected  

> show #!61 models

> show #!14 models

> show #!13 models

> hide #!14 models

> color zone #13 near sel distance 24

> hide #!13 models

> show #!14 models

> select clear

> hide #!14 models

> hide #!52 models

> show #!14 models

> hide #!61 models

> show #!58 models

> show #!53 models

> hide #!14 models

> show #!60 models

> hide #!60 models

> show #!61 models

> hide #!61 models

Drag select of 17445 residues, 11 pseudobonds  

> show #!61 models

> select add #61/eEF2:361

211301 atoms, 4 bonds, 11 pseudobonds, 17446 residues, 4 models selected  

> select up

211329 atoms, 33 bonds, 11 pseudobonds, 17450 residues, 4 models selected  

> select up

217865 atoms, 6695 bonds, 11 pseudobonds, 18287 residues, 4 models selected  

> show #!14 models

> color zone #14 near sel distance 24

> hide #!53 models

> hide #!58 models

> hide #!14 models

Drag select of 3285 residues, 10 pseudobonds  

> select up

125995 atoms, 138789 bonds, 10 pseudobonds, 7648 residues, 2 models selected  

> select down

37886 atoms, 10 pseudobonds, 3285 residues, 2 models selected  
Drag select of 3357 residues, 9 pseudobonds  

> select (sel & #61/eEF2

Expected an objects specifier or a keyword  

> select (sel & #61/eEF2)

4956 atoms, 5045 bonds, 639 residues, 1 model selected  

> hide #!61 models

> show #!58 models

> show #!53 models

Drag select of 17445 residues, 11 pseudobonds  

> show #!14 models

> color zone #14 near sel distance 24

> color zone #14 near sel distance 12

> select clear

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/202508_subunitcolouring.cxs

> hide #!53 models

> hide #!58 models

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/202508_subunitcolouring.cxs
> includeMaps true

No atoms selected for color zoning  

[Repeated 1 time(s)]

> hide #!14 models

> show #!61 models

Drag select of 3190 residues, 9 pseudobonds  

> select (sel & #61/eEF2)

4971 atoms, 5058 bonds, 641 residues, 1 model selected  

> hide #!61 models

> show #!53 models

Drag select of 377 residues  
Drag select of 29 residues  
Drag select of 74 residues  

> select subtract #53/m

7164 atoms, 5058 bonds, 1005 residues, 2 models selected  

> show #!58 models

> hide #!53 models

> show #!53 models

> hide #!58 models

Drag select of 69 residues  
Drag select of 76 residues  

> select add #53/m

8775 atoms, 6857 bonds, 68 pseudobonds, 1081 residues, 3 models selected  

> hide #!53 models

> show #!58 models

Drag select of 17005 residues, 11 pseudobonds  

> color zone #14 near sel distance 24

> show #!14 models

> hide #!58 models

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/202508_subunitcolouring.cxs
> includeMaps true

——— End of log from Tue Aug 12 16:26:11 2025 ———

> view name session-start

opened ChimeraX session  

> show #!61 models

> show #!53 models

> hide #!53 models

> show #!53 models

> show #!58 models

> ui tool show "Color Zone"

> color zone #14 near #58 distance 4

> color zone #14 near sel distance 24

> select clear

> hide #!58 models

> hide #!53 models

> hide #!14 models

> show #!14 models

> hide #!61 models

> hide #!14 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!12 models

> show #!8 models

> show #!9 models

> show #!10 models

> show #!11 models

> show #!13 models

> show #!14 models

> surface dust #8 size 40

> surface dust #9 size 40

> surface dust #10 size 40

> surface dust #11 size 40

> surface dust #12 size 40

> surface dust #13 size 40

> surface dust #14 size 40

> hide #!9 models

> hide #!10 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!11 models

> volume level 0.7

> volume splitbyzone #8

Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 0 as #1.1, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 1 as #1.2, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 2 as #1.3, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 3 as #1.4, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 4 as #1.5, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 5 as #1.6, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 6 as #1.7, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  

> volume #1.2 level 0.708

> volume #1.7 level 0.5358

> volume #1.7 level 0.5985

> lighting soft

> lighting full

> lighting simple

> lighting soft

> graphics silhouettes false

> lighting simple

> lighting full

> hide #!1 models

> show #!1 models

> lighting soft

> volume #1.7 color #911db4

> volume #1.7 color #cd29ff

> volume #1.7 color #b500ff

> volume #1.7 color #9437ff

> volume #1.7 color #ff40ff

> volume #1.7 color #d783ff

> volume #1.7 color #9437ff

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> save /Users/campbell/Desktop/image5.png supersample 3

> hide #!1 models

> show #!9 models

> show #!8 models

> hide #!8 models

> volume splitbyzone #9

Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 0 as #2.1, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 1 as #2.2, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 2 as #2.3, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 3 as #2.4, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 4 as #2.5, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  

> volume #1.7 level 0.5132

> volume #2.5 level 0.599

> lighting simple

> lighting full

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> volume #2.5 color #9437ff

> show #!1 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!8 models

> volume splitbyzone #8

Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 0 as #3.1, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 1 as #3.2, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 2 as #3.3, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 3 as #3.4, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 4 as #3.5, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 5 as #3.6, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 6 as #3.7, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  

> hide #!3 models

> show #!9 models

> volume splitbyzone #9

Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 0 as #4.1, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 1 as #4.2, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 2 as #4.3, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 3 as #4.4, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 4 as #4.5, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  

> close #4

> show #!3 models

> show #!1 models

> hide #!1 models

> close #3

> show #!1 models

> show #!2 models

> hide #!2 models

> show #!10 models

> hide #!1 models

> show #!58 models

> show #!52 models

> hide #!58 models

> show #!58 models

> hide #!10 models

Drag select of 17673 residues, 11 pseudobonds  

> select subtract #52/jj

212317 atoms, 11 pseudobonds, 17232 residues, 3 models selected  

> select subtract #52/ii

210701 atoms, 11 pseudobonds, 17156 residues, 3 models selected  

> show #!10 models

> color zone #10 near sel distance 24

> volume splitbyzone #10

Opened MultiPostProcessor_PPout_Post_E.mrc 0 as #3.1, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 1 as #3.2, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 2 as #3.3, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 3 as #3.4, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 4 as #3.5, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  

> hide #!3 models

> show #!11 models

> select clear

> hide #!52 models

> hide #!58 models

> volume splitbyzone #10

Opened MultiPostProcessor_PPout_Post_E.mrc 0 as #4.1, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 1 as #4.2, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 2 as #4.3, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 3 as #4.4, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 4 as #4.5, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  

> hide #!11 models

> show #!12 models

> volume splitbyzone #10

Opened MultiPostProcessor_PPout_Post_E.mrc 0 as #5.1, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 1 as #5.2, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 2 as #5.3, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 3 as #5.4, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 4 as #5.5, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  

> close #5

> hide #!4 models

> volume splitbyzone #12

Opened MultiPostProcessor_PPout_Rotated2.mrc 0 as #5.1, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 1 as #5.2, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 2 as #5.3, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 3 as #5.4, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 4 as #5.5, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 5 as #5.6, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  

> show #!13 models

> hide #!5 models

> volume splitbyzone #13

Opened MultiPostProcessor_PPout_Translocating_E.mrc 0 as #6.1, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 1 as #6.2, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 2 as #6.3, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 3 as #6.4, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 4 as #6.5, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 5 as #6.6, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  

> show #!14 models

> hide #!6 models

> volume splitbyzone #14

Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 0 as #7.1, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 1 as #7.2, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 2 as #7.3, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 3 as #7.4, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 4 as #7.5, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 5 as #7.6, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 6 as #7.7, grid size
128,128,128, pixel 4, shown at level 0.7, step 1, values float32  

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/202508_subunitcolouring.cxs
> includeMaps true

> lighting soft

> lighting simple

> lighting full

> hide #!7 models

> show #!1 models

> surface dust #1.2 size 40

> surface dust #1.3 size 40

> surface dust #1.4 size 40

> surface dust #1.5 size 40

> surface dust #1.6 size 40

> surface dust #1.7 size 40

> volume #1.7 color #d783ff

> volume #1.7 color #ff40ff

> volume #1.6 color #7a81ff

> volume #1.6 color #d783ff

> volume #1.6 color #9437ff

> volume #1.6 level 0.6143

> volume #1.7 level 0.527

> save /Users/campbell/Desktop/image3.png supersample 3

> hide #!1 models

> show #!2 models

> volume #2.4 level 0.6049

> volume #2.5 color #d783ff

> show #!1 models

> hide #!1 models

> show #!1 models

> volume #2.5 color #ff85ff

> volume #2.5 color #ff40ff

> hide #!1 models

> save /Users/campbell/Desktop/image4.png supersample 3

> hide #!2 models

> show #!3 models

> close #4

> show #!11 models

> hide #!3 models

> volume splitbyzone #11

Opened MultiPostProcessor_PPout_Rotated1.mrc 0 as #4.1, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 1 as #4.2, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 2 as #4.3, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 3 as #4.4, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 4 as #4.5, grid size 128,128,128,
pixel 4, shown at level 0.7, step 1, values float32  

> volume #4.2 level 0.5996

> volume #4.3 level 0.5785

> surface dust #4.1 size 40

> surface dust #4.2 size 40

> surface dust #4.3 size 40

> surface dust #4.4 size 40

> surface dust #4.5 size 40

> show #!3 models

> hide #!4 models

> volume #3.5 level 0.5994

> volume #3.2 level 0.6083

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!6 models

> show #!5 models

> hide #!6 models

> volume #5.2 level 0.6098

> volume #5.3 level 0.6438

> volume #5.5 level 0.6067

> hide #!5 models

> show #!6 models

> volume #6.4 level 0.6049

> volume #6.2 level 0.6319

> volume #6.5 level 0.6156

> hide #!6 models

> show #!7 models

> volume #7.7 color #ff40ff

> volume #7.7 level 0.6201

> volume #7.5 level 0.5693

> volume #7.4 level 0.6601

> show #!6 models

> hide #!7 models

> hide #!6 models

> show #!1 models

> save /Users/campbell/Desktop/image3.png supersample 3

> hide #!1 models

> show #!2 models

> save /Users/campbell/Desktop/image4.png supersample 3

> hide #!2 models

> show #!3 models

> save /Users/campbell/Desktop/image5.png supersample 3

> hide #!3 models

> show #!4 models

> save /Users/campbell/Desktop/image6.png supersample 3

> hide #!4 models

> show #!5 models

> save /Users/campbell/Desktop/image7.png supersample 3

> hide #!5 models

> show #!6 models

> save /Users/campbell/Desktop/image8.png supersample 3

> hide #!6 models

> show #!7 models

> save /Users/campbell/Desktop/image9.png supersample 3

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/202508_subunitcolouring.cxs
> includeMaps true

——— End of log from Tue Aug 12 16:48:18 2025 ———

> view name session-start

opened ChimeraX session  

> show #!50 models

> hide #!50 models

> show #!53 models

> hide #!7 models

> show #!58 models

> hide #!53 models

> hide #!58 models

> close #1-14

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Decoding1_E/MultiPostProcessor_PPout_Decoding1_E.mrc

Opened MultiPostProcessor_PPout_Decoding1_E.mrc as #1, grid size 128,128,128,
pixel 4, shown at level 0.882, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Decoding1_IF5/MultiPostProcessor_PPout_Decoding1_IF5.mrc

Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc as #2, grid size
128,128,128, pixel 4, shown at level 0.903, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Decoding1_open/MultiPostProcessor_PPout_Decoding1_open.mrc

Opened MultiPostProcessor_PPout_Decoding1_open.mrc as #3, grid size
128,128,128, pixel 4, shown at level 0.907, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Decoding2_E/MultiPostProcessor_PPout_Decoding2_E.mrc

Opened MultiPostProcessor_PPout_Decoding2_E.mrc as #4, grid size 128,128,128,
pixel 4, shown at level 0.904, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Decoding2_IF5/MultiPostProcessor_PPout_Decoding2_IF5.mrc

Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc as #5, grid size
128,128,128, pixel 4, shown at level 0.93, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Decoding2_open/MultiPostProcessor_PPout_Decoding2_open.mrc

Opened MultiPostProcessor_PPout_Decoding2_open.mrc as #6, grid size
128,128,128, pixel 4, shown at level 0.929, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Hibernating_E/MultiPostProcessor_PPout_Hibernating_E.mrc

Opened MultiPostProcessor_PPout_Hibernating_E.mrc as #7, grid size
128,128,128, pixel 4, shown at level 0.922, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Hibernating_IF5/MultiPostProcessor_PPout_Hibernating_IF5.mrc

Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc as #8, grid size
128,128,128, pixel 4, shown at level 0.945, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Hibernating_open/MultiPostProcessor_PPout_Hibernating_open.mrc

Opened MultiPostProcessor_PPout_Hibernating_open.mrc as #9, grid size
128,128,128, pixel 4, shown at level 0.871, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Post_E/MultiPostProcessor_PPout_Post_E.mrc

Opened MultiPostProcessor_PPout_Post_E.mrc as #10, grid size 128,128,128,
pixel 4, shown at level 0.839, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Post_IF5/MultiPostProcessor_PPout_Post_IF5.mrc

Opened MultiPostProcessor_PPout_Post_IF5.mrc as #11, grid size 128,128,128,
pixel 4, shown at level 0.861, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Post_open/MultiPostProcessor_PPout_Post_open.mrc

Opened MultiPostProcessor_PPout_Post_open.mrc as #12, grid size 128,128,128,
pixel 4, shown at level 0.856, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Rotated1/MultiPostProcessor_PPout_Rotated1.mrc

Opened MultiPostProcessor_PPout_Rotated1.mrc as #13, grid size 128,128,128,
pixel 4, shown at level 0.846, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Rotated2/MultiPostProcessor_PPout_Rotated2.mrc

Opened MultiPostProcessor_PPout_Rotated2.mrc as #14, grid size 128,128,128,
pixel 4, shown at level 0.872, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Translocating_E/MultiPostProcessor_PPout_Translocating_E.mrc

Opened MultiPostProcessor_PPout_Translocating_E.mrc as #15, grid size
128,128,128, pixel 4, shown at level 0.888, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Translocating_IF5/MultiPostProcessor_PPout_Translocating_IF5.mrc

Opened MultiPostProcessor_PPout_Translocating_IF5.mrc as #16, grid size
128,128,128, pixel 4, shown at level 0.87, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/Translocating_open/MultiPostProcessor_PPout_Translocating_open.mrc

Opened MultiPostProcessor_PPout_Translocating_open.mrc as #17, grid size
128,128,128, pixel 4, shown at level 0.879, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/UnrotatedPre_cEF2_IF5/MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc

Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc as #18, grid size
128,128,128, pixel 4, shown at level 0.913, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/Comb25_Subclass/UnrotatedPre_none_IF5/MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc

Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc as #19, grid size
128,128,128, pixel 4, shown at level 0.899, step 1, values float32  

> volume #1-49 level 0.65

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> hide #!17 models

> hide #!18 models

> hide #!19 models

> show #!4 models

> hide #!1 models

> volume #1-49 level 0.6

> show #!1 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> show #!1 models

> hide #!4 models

> show #!4 models

> lighting soft

> hide #!1 models

> show #!1 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> hide #!4 models

> show #!2 models

> lighting simple

> show #!5 models

> hide #!2 models

> show #!1 models

> show #!6 models

> hide #!5 models

> hide #!1 models

> show #!3 models

> hide #!6 models

> volume #3 level 0.237

> volume #3 level 0.6

> hide #!3 models

> show #!5 models

> fitmap #1-49 inMap #50 eachModel true

Fit map MultiPostProcessor_PPout_Decoding1_E.mrc in map Stable_60S.mrc using
59402 points  
correlation = 0.7911, correlation about mean = 0.327, overlap = 2.791e+04  
steps = 88, shift = 1.87, angle = 1.28 degrees  
  
Position of MultiPostProcessor_PPout_Decoding1_E.mrc (#1) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99976874 0.01805251 0.01168621 -7.96458213  
-0.01812410 0.99981745 0.00604905 4.56676329  
-0.01157488 -0.00625945 0.99991342 3.68282798  
Axis -0.27513543 0.51996175 -0.80866574  
Axis point 202.19610879 419.58198075 0.00000000  
Rotation angle (degrees) 1.28170368  
Shift along axis 1.58770413  
  
Fit map MultiPostProcessor_PPout_Decoding1_IF5.mrc in map Stable_60S.mrc using
59281 points  
correlation = 0.7914, correlation about mean = 0.3231, overlap = 2.868e+04  
steps = 64, shift = 1.74, angle = 1.3 degrees  
  
Position of MultiPostProcessor_PPout_Decoding1_IF5.mrc (#2) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99976169 0.01831848 0.01187391 -8.04472940  
-0.01838834 0.99981409 0.00580117 4.59637574  
-0.01176544 -0.00601813 0.99991267 3.75422902  
Axis -0.26130589 0.52262812 -0.81152885  
Axis point 204.27550108 421.02370601 0.00000000  
Rotation angle (degrees) 1.29590266  
Shift along axis 1.45766526  
  
Fit map MultiPostProcessor_PPout_Decoding1_open.mrc in map Stable_60S.mrc
using 63787 points  
correlation = 0.7918, correlation about mean = 0.3197, overlap = 2.976e+04  
steps = 76, shift = 2.02, angle = 1.33 degrees  
  
Position of MultiPostProcessor_PPout_Decoding1_open.mrc (#3) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99974821 0.01902926 0.01189116 -8.30287687  
-0.01909710 0.99980185 0.00561799 4.96489118  
-0.01178190 -0.00584366 0.99991352 3.40070465  
Axis -0.24745292 0.51109301 -0.82313485  
Axis point 207.68564282 415.75565299 0.00000000  
Rotation angle (degrees) 1.32704564  
Shift along axis 1.79285377  
  
Fit map MultiPostProcessor_PPout_Decoding2_E.mrc in map Stable_60S.mrc using
59129 points  
correlation = 0.7912, correlation about mean = 0.3363, overlap = 2.869e+04  
steps = 64, shift = 1.73, angle = 1.25 degrees  
  
Position of MultiPostProcessor_PPout_Decoding2_E.mrc (#4) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99977714 0.01788998 0.01120805 -7.66665206  
-0.01795003 0.99982494 0.00528084 4.71552034  
-0.01111161 -0.00548085 0.99992324 3.65246377  
Axis -0.24698854 0.51225214 -0.82255359  
Axis point 221.43702062 413.28954814 0.00000000  
Rotation angle (degrees) 1.24833428  
Shift along axis 1.30476338  
  
Fit map MultiPostProcessor_PPout_Decoding2_IF5.mrc in map Stable_60S.mrc using
59486 points  
correlation = 0.7898, correlation about mean = 0.3255, overlap = 2.952e+04  
steps = 64, shift = 1.68, angle = 1.28 degrees  
  
Position of MultiPostProcessor_PPout_Decoding2_IF5.mrc (#5) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99976397 0.01860026 0.01122686 -7.81996437  
-0.01865785 0.99981319 0.00504636 4.91861513  
-0.01113090 -0.00525464 0.99992424 3.63276708  
Axis -0.23067534 0.50066776 -0.83433847  
Axis point 226.38325290 407.97261497 0.00000000  
Rotation angle (degrees) 1.27940265  
Shift along axis 1.23550762  
  
Fit map MultiPostProcessor_PPout_Decoding2_open.mrc in map Stable_60S.mrc
using 63326 points  
correlation = 0.7903, correlation about mean = 0.3304, overlap = 3.035e+04  
steps = 52, shift = 1.77, angle = 1.34 degrees  
  
Position of MultiPostProcessor_PPout_Decoding2_open.mrc (#6) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99974213 0.01949630 0.01164297 -8.09518726  
-0.01955682 0.99979570 0.00510701 5.20545430  
-0.01154103 -0.00533340 0.99991918 3.64105673  
Axis -0.22403863 0.49750082 -0.83803319  
Axis point 227.57030898 402.68989381 -0.00000000  
Rotation angle (degrees) 1.33513908  
Shift along axis 1.35202601  
  
Fit map MultiPostProcessor_PPout_Hibernating_E.mrc in map Stable_60S.mrc using
62275 points  
correlation = 0.7964, correlation about mean = 0.3603, overlap = 3.011e+04  
steps = 52, shift = 2, angle = 0.212 degrees  
  
Position of MultiPostProcessor_PPout_Hibernating_E.mrc (#7) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99999321 0.00326153 0.00171439 -2.21888443  
-0.00326114 0.99999466 -0.00023095 2.56192559  
-0.00171513 0.00022535 0.99999850 0.02699344  
Axis 0.06180080 0.46448828 -0.88342023  
Axis point 637.87925896 701.14479383 0.00000000  
Rotation angle (degrees) 0.21152040  
Shift along axis 1.02900904  
  
Fit map MultiPostProcessor_PPout_Hibernating_IF5.mrc in map Stable_60S.mrc
using 63153 points  
correlation = 0.7951, correlation about mean = 0.3571, overlap = 3.106e+04  
steps = 56, shift = 2.13, angle = 0.404 degrees  
  
Position of MultiPostProcessor_PPout_Hibernating_IF5.mrc (#8) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99998335 0.00399359 0.00416445 -2.88996695  
-0.00401047 0.99998375 0.00405231 1.89960466  
-0.00414820 -0.00406894 0.99998312 1.76556607  
Axis -0.57552687 0.58909134 -0.56722149  
Axis point 667.29705654 0.00000000 450.51779174  
Rotation angle (degrees) 0.40425323  
Shift along axis 1.78082725  
  
Fit map MultiPostProcessor_PPout_Hibernating_open.mrc in map Stable_60S.mrc
using 60547 points  
correlation = 0.8152, correlation about mean = 0.3987, overlap = 2.89e+04  
steps = 72, shift = 2.15, angle = 0.463 degrees  
  
Position of MultiPostProcessor_PPout_Hibernating_open.mrc (#9) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99997363 0.00591366 0.00421433 -3.47155336  
-0.00592859 0.99997616 0.00354043 2.40622389  
-0.00419329 -0.00356532 0.99998485 1.33190491  
Axis -0.43948266 0.52000174 -0.73242965  
Axis point 246.03840628 454.26301712 0.00000000  
Rotation angle (degrees) 0.46319695  
Shift along axis 1.80140146  
  
Fit map MultiPostProcessor_PPout_Post_E.mrc in map Stable_60S.mrc using 60107
points  
correlation = 0.7977, correlation about mean = 0.318, overlap = 2.695e+04  
steps = 104, shift = 2, angle = 1.09 degrees  
  
Position of MultiPostProcessor_PPout_Post_E.mrc (#10) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99982744 0.01371127 0.01253378 -7.21702630  
-0.01375872 0.99989847 0.00370712 4.05104519  
-0.01248168 -0.00387893 0.99991458 3.11397695  
Axis -0.20005445 0.65969141 -0.72442078  
Axis point 201.53103384 501.74928587 0.00000000  
Rotation angle (degrees) 1.08639112  
Shift along axis 1.86040835  
  
Fit map MultiPostProcessor_PPout_Post_IF5.mrc in map Stable_60S.mrc using
60639 points  
correlation = 0.7956, correlation about mean = 0.3097, overlap = 2.773e+04  
steps = 68, shift = 1.86, angle = 1.1 degrees  
  
Position of MultiPostProcessor_PPout_Post_IF5.mrc (#11) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99982585 0.01439549 0.01187585 -7.13509603  
-0.01444969 0.99988551 0.00449092 3.98676733  
-0.01180984 -0.00466174 0.99991939 3.30610554  
Axis -0.23816755 0.61634108 -0.75059968  
Axis point 200.73424655 470.36423178 0.00000000  
Rotation angle (degrees) 1.10099234  
Shift along axis 1.67499509  
  
Fit map MultiPostProcessor_PPout_Post_open.mrc in map Stable_60S.mrc using
62418 points  
correlation = 0.795, correlation about mean = 0.2943, overlap = 2.778e+04  
steps = 72, shift = 2.43, angle = 0.991 degrees  
  
Position of MultiPostProcessor_PPout_Post_open.mrc (#12) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99986233 0.01100900 0.01241434 -6.59251481  
-0.01106976 0.99992703 0.00483637 3.41572075  
-0.01236019 -0.00497312 0.99991124 3.01347904  
Axis -0.28347400 0.71593260 -0.63803057  
Axis point 363.80595606 0.00000000 480.46532160  
Rotation angle (degrees) 0.99139688  
Shift along axis 2.39154063  
  
Fit map MultiPostProcessor_PPout_Rotated1.mrc in map Stable_60S.mrc using
56561 points  
correlation = 0.8025, correlation about mean = 0.3245, overlap = 2.656e+04  
steps = 84, shift = 2.21, angle = 0.299 degrees  
  
Position of MultiPostProcessor_PPout_Rotated1.mrc (#13) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99999877 0.00066264 -0.00141870 -1.10491254  
-0.00066971 0.99998736 -0.00498347 3.14612435  
0.00141538 0.00498441 0.99998658 -1.97454050  
Axis 0.95402431 -0.27124992 -0.12751899  
Axis point 0.00000000 439.95627731 540.07575665  
Rotation angle (degrees) 0.29932172  
Shift along axis -1.65570799  
  
Fit map MultiPostProcessor_PPout_Rotated2.mrc in map Stable_60S.mrc using
55876 points  
correlation = 0.7965, correlation about mean = 0.3517, overlap = 2.697e+04  
steps = 52, shift = 2.02, angle = 0.557 degrees  
  
Position of MultiPostProcessor_PPout_Rotated2.mrc (#14) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99997820 0.00283253 -0.00596421 -0.55492718  
-0.00287500 0.99997049 -0.00712463 3.98347982  
0.00594385 0.00714162 0.99995683 -3.24244224  
Axis 0.73387023 -0.61256256 -0.29360107  
Axis point 0.00000000 534.32330989 393.93820254  
Rotation angle (degrees) 0.55691667  
Shift along axis -1.89539064  
  
Fit map MultiPostProcessor_PPout_Translocating_E.mrc in map Stable_60S.mrc
using 58868 points  
correlation = 0.7979, correlation about mean = 0.3674, overlap = 2.84e+04  
steps = 80, shift = 1.98, angle = 0.696 degrees  
  
Position of MultiPostProcessor_PPout_Translocating_E.mrc (#15) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99993288 0.01035511 0.00519701 -4.62869601  
-0.01037408 0.99993958 0.00363590 3.43941422  
-0.00515905 -0.00368957 0.99997989 1.98852097  
Axis -0.30142925 0.42613230 -0.85296640  
Axis point 281.27959097 414.91524566 0.00000000  
Rotation angle (degrees) 0.69623142  
Shift along axis 1.16472830  
  
Fit map MultiPostProcessor_PPout_Translocating_IF5.mrc in map Stable_60S.mrc
using 63215 points  
correlation = 0.802, correlation about mean = 0.3522, overlap = 2.898e+04  
steps = 88, shift = 2, angle = 0.765 degrees  
  
Position of MultiPostProcessor_PPout_Translocating_IF5.mrc (#16) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99991795 0.01004081 0.00795429 -5.32499458  
-0.01007051 0.99994244 0.00370276 3.30361218  
-0.00791665 -0.00378256 0.99996151 2.56435892  
Axis -0.28044864 0.59462919 -0.75350162  
Axis point 235.16990017 489.64640778 0.00000000  
Rotation angle (degrees) 0.76464884  
Shift along axis 1.52556309  
  
Fit map MultiPostProcessor_PPout_Translocating_open.mrc in map Stable_60S.mrc
using 64454 points  
correlation = 0.7986, correlation about mean = 0.3522, overlap = 2.929e+04  
steps = 56, shift = 2.12, angle = 0.529 degrees  
  
Position of MultiPostProcessor_PPout_Translocating_open.mrc (#17) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99996290 0.00783096 0.00358791 -3.71300564  
-0.00784276 0.99996384 0.00328730 3.00234171  
-0.00356203 -0.00331532 0.99998816 1.38036757  
Axis -0.35787617 0.38754248 -0.84955016  
Axis point 315.69331386 415.33223041 0.00000000  
Rotation angle (degrees) 0.52854493  
Shift along axis 1.31963970  
  
Fit map MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc in map
Stable_60S.mrc using 58278 points  
correlation = 0.7868, correlation about mean = 0.3156, overlap = 2.842e+04  
steps = 64, shift = 2.56, angle = 0.963 degrees  
  
Position of MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc (#18) relative
to Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99992656 0.00215832 0.01192513 -4.02215773  
-0.00229700 0.99992976 0.01162790 0.14047040  
-0.01189920 -0.01165443 0.99986128 5.37646741  
Axis -0.69275610 0.70888307 -0.13256612  
Axis point 473.55149272 0.00000000 213.95372323  
Rotation angle (degrees) 0.96285115  
Shift along axis 2.17321395  
  
Fit map MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc in map
Stable_60S.mrc using 57953 points  
correlation = 0.793, correlation about mean = 0.3182, overlap = 2.823e+04  
steps = 120, shift = 2.23, angle = 0.887 degrees  
  
Position of MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc (#19) relative
to Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99991650 0.00685207 0.01095655 -5.03219678  
-0.00694507 0.99993999 0.00847293 1.68244680  
-0.01089783 -0.00854832 0.99990408 4.29067316  
Axis -0.55001840 0.70619421 -0.44583573  
Axis point 474.12641037 0.00000000 360.34159610  
Rotation angle (degrees) 0.88659304  
Shift along axis 2.04299963  
  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!5 models

> show #!1 models

> ui tool show "Color Zone"

> show #!58 models

> hide #!1 models

> show #!1 models

> show #!52 models

> select add #52

220934 atoms, 236952 bonds, 5887 pseudobonds, 18186 residues, 4 models
selected  

> select add #58

430070 atoms, 461671 bonds, 10400 pseudobonds, 35268 residues, 7 models
selected  

> color zone #1 near sel distance 30

> hide #!1 models

Drag select of 17673 residues, 11 pseudobonds  

> show #!1 models

> color zone #1 near sel distance 30

> volume splitbyzone #1

Opened MultiPostProcessor_PPout_Decoding1_E.mrc 0 as #20.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 1 as #20.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 2 as #20.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 3 as #20.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 4 as #20.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 5 as #20.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_E.mrc 6 as #20.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!20 models

> show #!2 models

> show #!53 models

> select subtract #52/G

215700 atoms, 11 pseudobonds, 17673 residues, 3 models selected  

> hide #!2 models

> lighting soft

Drag select of 18075 residues, 10 pseudobonds  

> hide #!52 models

> hide #!58 models

> hide #!53 models

> select clear

> show #!58 models

> show #!52 models

> show #!53 models

Drag select of 18113 residues, 11 pseudobonds  

> select subtract #53/m

217893 atoms, 11 pseudobonds, 18037 residues, 4 models selected  
Drag select of 18113 residues, 11 pseudobonds  

> select #53/m:47

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

> select up

1611 atoms, 1799 bonds, 76 residues, 1 model selected  
Drag select of 18113 residues, 11 pseudobonds  

> select subtract #53/m

217893 atoms, 11 pseudobonds, 18037 residues, 4 models selected  

> hide #!53 models

> show #!53 models

> hide #!53 models

> show #!53 models

> select subtract #52/3

216300 atoms, 11 pseudobonds, 17962 residues, 4 models selected  

> show #!2 models

> color zone #2 near sel distance 24

> volume splitbyzone #2

Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 0 as #21.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 1 as #21.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 2 as #21.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 3 as #21.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 4 as #21.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 5 as #21.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_IF5.mrc 6 as #21.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!21 models

> show #!3 models

> hide #!3 models

> select subtract #53/eI

215157 atoms, 11 pseudobonds, 17808 residues, 4 models selected  

> show #!3 models

> color zone #3 near sel distance 30

> volume splitbyzone #3

Opened MultiPostProcessor_PPout_Decoding1_open.mrc 0 as #22.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 1 as #22.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 2 as #22.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 3 as #22.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 4 as #22.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding1_open.mrc 5 as #22.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!21.1 models

> show #!4 models

> select add #53

419069 atoms, 220182 bonds, 5241 pseudobonds, 34496 residues, 7 models
selected  

> select subtract #53

214107 atoms, 11 pseudobonds, 17598 residues, 3 models selected  

> select add #52/3

215700 atoms, 1779 bonds, 75 pseudobonds, 17673 residues, 4 models selected  

> hide #!22 models

> color zone #4 near sel distance 24

> volume splitbyzone #4

Opened MultiPostProcessor_PPout_Decoding2_E.mrc 0 as #23.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 1 as #23.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 2 as #23.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 3 as #23.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 4 as #23.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 5 as #23.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_E.mrc 6 as #23.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!23 models

> show #!5 models

> select subtract #52/3

214107 atoms, 11 pseudobonds, 17598 residues, 3 models selected  

> hide #!5 models

Drag select of 18113 residues, 11 pseudobonds  

> select subtract #53/m

217893 atoms, 11 pseudobonds, 18037 residues, 4 models selected  

> select subtract #52/3

216300 atoms, 11 pseudobonds, 17962 residues, 4 models selected  

> show #!5 models

> color zone #5 near sel distance 24

> hide #!52 models

> hide #!53 models

> hide #!58 models

> lighting soft

> lighting simple

> show #!52 models

> show #!53 models

> show #!58 models

> volume splitbyzone #5

Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 0 as #24.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 1 as #24.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 2 as #24.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 3 as #24.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 4 as #24.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 5 as #24.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_IF5.mrc 6 as #24.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!24 models

> show #!6 models

> select subtract #53/eI

215157 atoms, 11 pseudobonds, 17808 residues, 4 models selected  

> color zone #6 near sel distance 24

> volume splitbyzone #6

Opened MultiPostProcessor_PPout_Decoding2_open.mrc 0 as #25.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 1 as #25.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 2 as #25.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 3 as #25.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 4 as #25.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding2_open.mrc 5 as #25.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!25 models

> show #!7 models

> show #!61 models

> hide #!58 models

> hide #!53 models

> hide #!52 models

> show #!52 models

> select add #61

422223 atoms, 221714 bonds, 5080 pseudobonds, 35411 residues, 8 models
selected  

> select add #58

423867 atoms, 446433 bonds, 9582 pseudobonds, 35488 residues, 9 models
selected  

> select subtract #58

214731 atoms, 221714 bonds, 5069 pseudobonds, 18406 residues, 6 models
selected  

> select add #53

418643 atoms, 441896 bonds, 10299 pseudobonds, 35094 residues, 9 models
selected  

> select subtract #53

213681 atoms, 221714 bonds, 5069 pseudobonds, 18196 residues, 5 models
selected  

> select add #52

428000 atoms, 458666 bonds, 10956 pseudobonds, 35789 residues, 8 models
selected  

> select subtract #52

207066 atoms, 221714 bonds, 5069 pseudobonds, 17603 residues, 4 models
selected  

> color zone #7 near sel distance 24

> volume splitbyzone #7

Opened MultiPostProcessor_PPout_Hibernating_E.mrc 0 as #26.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 1 as #26.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 2 as #26.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 3 as #26.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 4 as #26.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> select add #52/3

208659 atoms, 223493 bonds, 5133 pseudobonds, 17678 residues, 6 models
selected  

> close #26

> show #!7 models

> color zone #7 near sel distance 24

> volume splitbyzone #7

Opened MultiPostProcessor_PPout_Hibernating_E.mrc 0 as #26.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 1 as #26.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 2 as #26.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 3 as #26.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 4 as #26.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 5 as #26.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!61 models

> close #26

> show #!7 models

> select #52/3:53

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1593 atoms, 1779 bonds, 75 residues, 1 model selected  

> hide #!52 models

> show #!61 models

> hide #!7 models

Drag select of 16942 residues, 28 pseudobonds  

> show #!52 models

> hide #!61 models

> show #!61 models

> hide #!52 models

> show #!52 models

> show #!7 models

> color zone #7 near sel distance 24

> show #!53 models

> hide #!7 models

> graphics silhouettes false

> graphics silhouettes true

> hide #!53 models

> show #!53 models

> hide #!53 models

> show #!60 models

> hide #!60 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!58 models

> hide #!52 models

> show #!52 models

> hide #!52 models

> show #!52 models

> hide #!52 models

> select #58/L1:176

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

> select clear

> hide #!61 models

> show #!61 models

> hide #!61 models

> show #!61 models

> select add #61

207066 atoms, 221714 bonds, 5069 pseudobonds, 17603 residues, 4 models
selected  

> select add #58

416202 atoms, 446433 bonds, 9582 pseudobonds, 34685 residues, 7 models
selected  

> select sub#58/PT

Expected an objects specifier or a keyword  

> select subtract #58/PT

414558 atoms, 444597 bonds, 9501 pseudobonds, 34608 residues, 7 models
selected  

> show #!52 models

> select add #52/3

416151 atoms, 446376 bonds, 9565 pseudobonds, 34683 residues, 9 models
selected  

> show #!7 models

> color zone #7 near sel distance 24

> hide #!61 models

> show #!61 models

> hide #!61 models

> hide #!52 models

> hide #!58 models

> select subtract #61

209085 atoms, 224662 bonds, 4496 pseudobonds, 17080 residues, 5 models
selected  

> show #!61 models

> hide #!7 models

Drag select of 16942 residues, 28 pseudobonds  

> show #!58 models

> show #!52 models

> show #!7 models

> color zone #7 near sel distance 24

[Repeated 2 time(s)]

> hide #!58 models

> show #!58 models

> hide #!58 models

> show #!58 models

> hide #!7 models

> show sel cartoons

> hide #!58 models

> show #!58 models

> undo

[Repeated 2 time(s)]

> select add #58

413976 atoms, 226498 bonds, 4605 pseudobonds, 34099 residues, 7 models
selected  

> select subtract #58

204840 atoms, 1779 bonds, 92 pseudobonds, 17017 residues, 4 models selected  

> hide #!52 models

> show #!52 models

> hide #!52 models

> hide #!61 models

Drag select of 17005 residues, 11 pseudobonds  

> show #!61 models

> show #!52 models

> select subtract #52/2

412332 atoms, 1779 bonds, 103 pseudobonds, 34022 residues, 6 models selected  

> hide #!52 models

> select subtract #58/PT

410688 atoms, 1779 bonds, 103 pseudobonds, 33945 residues, 6 models selected  

> hide #!58 models

> show #!52 models

> show #!7 models

> color zone #7 near sel distance 24

> volume splitbyzone #7

Opened MultiPostProcessor_PPout_Hibernating_E.mrc 0 as #26.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 1 as #26.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 2 as #26.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 3 as #26.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_E.mrc 4 as #26.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!26 models

> show #!8 models

> hide #!52 models

> select add #52

630029 atoms, 236952 bonds, 5926 pseudobonds, 52056 residues, 8 models
selected  

> select subtract #52

409095 atoms, 39 pseudobonds, 33870 residues, 4 models selected  

> select add #58

412383 atoms, 224719 bonds, 4541 pseudobonds, 34024 residues, 5 models
selected  

> select subtract #58

203247 atoms, 28 pseudobonds, 16942 residues, 2 models selected  

> show #!53 models

> hide #!8 models

> select add #53

408209 atoms, 220182 bonds, 5258 pseudobonds, 33840 residues, 6 models
selected  

> select subtract #53

203247 atoms, 28 pseudobonds, 16942 residues, 2 models selected  

> hide #!61 models

Drag select of 364 residues  

> show #!61 models

> show #!8 models

> color zone #8 near sel distance 24

> volume splitbyzone #8

Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 0 as #27.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 1 as #27.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 2 as #27.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 3 as #27.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_IF5.mrc 4 as #27.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!27 models

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/Manuscript1/202512_subunitcolouring.cxs
> includeMaps true

> show #!9 models

> hide #!53 models

> select add #53

408209 atoms, 220182 bonds, 5258 pseudobonds, 33840 residues, 6 models
selected  

> select subtract #53

203247 atoms, 28 pseudobonds, 16942 residues, 2 models selected  

> show #!60 models

> hide #!60 models

> color zone #9 near sel distance 36

> volume splitbyzone #9

Opened MultiPostProcessor_PPout_Hibernating_open.mrc 0 as #28.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc 1 as #28.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc 2 as #28.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc 3 as #28.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> close #28

> show #!9 models

> color zone #9 near sel distance 4

> color zone #9 near sel distance 48

> color zone #9 near sel distance 488

> color zone #9 near sel distance 48

> volume splitbyzone #9

Opened MultiPostProcessor_PPout_Hibernating_open.mrc 0 as #28.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc 1 as #28.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc 2 as #28.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating_open.mrc 3 as #28.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!28 models

> show #!9 models

> hide #!9 models

> show #!10 models

> show #!11 models

> show #!12 models

> hide #!12 models

> hide #!11 models

> hide #!61 models

> select add #61

207066 atoms, 221714 bonds, 5069 pseudobonds, 17603 residues, 4 models
selected  

> select subtract #61

Nothing selected  

> show #!58 models

> show #!52 models

> hide #!52 models

> show #!52 models

> hide #!52 models

> select add #58

209136 atoms, 224719 bonds, 4513 pseudobonds, 17082 residues, 3 models
selected  

> color zone #9 near sel distance 24

> color zone #10 near sel distance 24

> select subtract #58

Nothing selected  

> show #!28 models

> hide #!28 models

> show #!9 models

> hide #!10 models

> color single #9

> hide #!58 models

> show #!61 models

> hide #!9 models

Drag select of 16942 residues, 28 pseudobonds  

> show #!9 models

> show #!59 models

> hide #!59 models

> show #!59 models

> hide #!59 models

> show #!60 models

> hide #!60 models

> show #!58 models

> hide #!58 models

> show #!59 models

> hide #!59 models

> show #!60 models

> hide #!60 models

> color zone #9 near sel distance 48

> select clear

> hide #!9 models

> show #!10 models

> hide #!61 models

> show #!52 models

> show #!58 models

> hide #!10 models

> hide #!52 models

Drag select of 16976 residues, 10 pseudobonds  
Drag select of 17005 residues, 11 pseudobonds  

> show #!52 models

> select add #52/3

209085 atoms, 1779 bonds, 75 pseudobonds, 17080 residues, 4 models selected  

> show #!10 models

> color zone #10 near sel distance 24

> volume splitbyzone #10

Opened MultiPostProcessor_PPout_Post_E.mrc 0 as #29.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 1 as #29.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 2 as #29.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 3 as #29.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_E.mrc 4 as #29.5, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  

> hide #!29 models

> show #!11 models

> select add #52

428426 atoms, 236952 bonds, 5898 pseudobonds, 35191 residues, 6 models
selected  

> select subtract #52

207492 atoms, 11 pseudobonds, 17005 residues, 2 models selected  

> hide #!52 models

> show #!53 models

> hide #!58 models

> hide #!11 models

Drag select of 364 residues  

> show #!58 models

> show #!12 models

> hide #!12 models

> show #!11 models

> color zone #11 near sel distance 24

> volume splitbyzone #11

Opened MultiPostProcessor_PPout_Post_IF5.mrc 0 as #30.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc 1 as #30.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc 2 as #30.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc 3 as #30.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_IF5.mrc 4 as #30.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!30 models

> show #!12 models

> select subtract #53/eI

208542 atoms, 11 pseudobonds, 17215 residues, 3 models selected  

> color zone #12 near sel distance 24

> volume splitbyzone #12

Opened MultiPostProcessor_PPout_Post_open.mrc 0 as #31.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_open.mrc 1 as #31.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_open.mrc 2 as #31.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post_open.mrc 3 as #31.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!31 models

> show #!9 models

> show #!12 models

> hide #!9 models

> show #!9 models

> hide #!12 models

> hide #!9 models

> show #!11 models

> show #!13 models

> hide #!11 models

> hide #!53 models

> hide #!58 models

> select add #58

210186 atoms, 224719 bonds, 4513 pseudobonds, 17292 residues, 4 models
selected  

> select subtract #58

1050 atoms, 210 residues, 1 model selected  

> select add #53

204962 atoms, 220182 bonds, 5230 pseudobonds, 16898 residues, 4 models
selected  

> select subtract #53

Nothing selected  

> show #!59 models

> show #!51 models

> show #!52 models

> hide #!13 models

> show #!13 models

> hide #!52 models

> show #!53 models

> show #!14 models

> hide #!13 models

> show #!13 models

> hide #!51 models

> hide #!53 models

> hide #!59 models

> show #!17 models

> hide #!17 models

> show #!18 models

> hide #!13 models

> show #!13 models

> hide #!18 models

> hide #!14 models

> show #!51 models

> show #!59 models

> hide #!51 models

> show #!51 models

> hide #!51 models

> show #!51 models

> hide #!59 models

> show #!59 models

> hide #!59 models

> show #!59 models

> hide #!51 models

> show #!51 models

> hide #!59 models

> hide #!13 models

Drag select of 17638 residues, 20 pseudobonds  

> select subtract #51/33

217771 atoms, 20 pseudobonds, 17563 residues, 2 models selected  

> select subtract #51/q3

216192 atoms, 20 pseudobonds, 17489 residues, 2 models selected  

> hide sel cartoons

> select clear

Drag select of 149 residues  

> show #!59 models

> show #!58 models

> hide #!59 models

> show #!61 models

> hide #!58 models

> show #!59 models

> hide #!61 models

Drag select of 2261 residues, 1 pseudobonds  

> select (sel & #59/74)

568 atoms, 569 bonds, 72 residues, 1 model selected  

> color sel gray

> color sel dark gray

> color sel dim gray

> select clear

Drag select of 17213 residues, 12 pseudobonds  

> show #!13 models

> color zone #12 near sel distance 24

> show #!12 models

> hide #!13 models

> undo

[Repeated 1 time(s)]

> show #!12 models

> hide #!13 models

> undo

[Repeated 3 time(s)]

> show #!12 models

> hide #!12 models

> show #!13 models

> color zone #13 near sel distance 24

> volume splitbyzone #13

Opened MultiPostProcessor_PPout_Rotated1.mrc 0 as #32.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 1 as #32.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 2 as #32.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 3 as #32.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated1.mrc 4 as #32.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!32 models

> show #!14 models

> show #!61 models

> select add #61/eEF2

217541 atoms, 6729 bonds, 19 pseudobonds, 18062 residues, 5 models selected  

> color zone #14 near sel distance 24

> volume splitbyzone #14

Opened MultiPostProcessor_PPout_Rotated2.mrc 0 as #33.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 1 as #33.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 2 as #33.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 3 as #33.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 4 as #33.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 5 as #33.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 6 as #33.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!33 models

> show #!15 models

> hide #!51 models

> show #!52 models

> show #!51 models

> hide #!51 models

> select add #51

434041 atoms, 242506 bonds, 3994 pseudobonds, 35859 residues, 8 models
selected  

> select subtract #51

214358 atoms, 6729 bonds, 19 pseudobonds, 17913 residues, 4 models selected  

> hide #!61 models

> show #!58 models

> hide #!59 models

> select add #59

214358 atoms, 229836 bonds, 4435 pseudobonds, 17913 residues, 5 models
selected  

> select subtract #59

6607 atoms, 6729 bonds, 7 pseudobonds, 849 residues, 2 models selected  

> select add #61

207066 atoms, 221714 bonds, 5069 pseudobonds, 17603 residues, 4 models
selected  

> select subtract #61

Nothing selected  

> show #!59 models

> hide #!59 models

> hide #!58 models

> show #!14 models

> show #!13 models

> hide #!14 models

> hide #!13 models

> show #!5 models

> hide #!5 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!58 models

> show #!61 models

> hide #!15 models

> hide #!52 models

> hide #!61 models

Drag select of 17005 residues, 11 pseudobonds  

> hide #!58 models

> show #!61 models

> select add #61/eEF2

214099 atoms, 6729 bonds, 18 pseudobonds, 17854 residues, 4 models selected  

> hide #!61 models

> show #!58 models

> show #!52 models

> show #!61 models

> hide #!52 models

> hide #!61 models

> show #!61 models

> show #!52 models

> select add #52/3

215692 atoms, 8508 bonds, 82 pseudobonds, 17929 residues, 6 models selected  

> show #!10 models

> show #!15 models

> hide #!10 models

> color zone #15 near sel distance 24

> volume splitbyzone #15

Opened MultiPostProcessor_PPout_Translocating_E.mrc 0 as #34.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 1 as #34.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 2 as #34.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 3 as #34.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 4 as #34.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 5 as #34.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_E.mrc 6 as #34.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!34 models

> show #!16 models

> select subtract #52/3

214099 atoms, 6729 bonds, 18 pseudobonds, 17854 residues, 4 models selected  

> hide #!52 models

> show #!53 models

> hide #!58 models

> hide #!61 models

> hide #!16 models

Drag select of 364 residues  

> show #!58 models

> show #!61 models

> show #!16 models

> color zone #16 near sel distance 24

> volume splitbyzone #16

Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 0 as #35.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 1 as #35.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 2 as #35.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 3 as #35.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 4 as #35.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 5 as #35.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_IF5.mrc 6 as #35.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!35 models

> show #!17 models

> select add #53

419061 atoms, 226911 bonds, 5248 pseudobonds, 34752 residues, 8 models
selected  

> select subtract #53

214099 atoms, 6729 bonds, 18 pseudobonds, 17854 residues, 4 models selected  

> hide #!53 models

> volume #17 level 0.5227

> volume #17 level 0.4487

> volume #17 level 0.4991

> volume #17 level 0.5

> color zone #17 near sel distance 24

> volume splitbyzone #17

Opened MultiPostProcessor_PPout_Translocating_open.mrc 0 as #36.1, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 1 as #36.2, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 2 as #36.3, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 3 as #36.4, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 4 as #36.5, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating_open.mrc 5 as #36.6, grid size
128,128,128, pixel 4, shown at level 0.5, step 1, values float32  

> hide #!36 models

> show #!18 models

> hide #!61 models

> select add #61

414558 atoms, 221714 bonds, 5080 pseudobonds, 34608 residues, 6 models
selected  

> select subtract #61

207492 atoms, 11 pseudobonds, 17005 residues, 2 models selected  

> show #!61 models

> select add #61/eEF2

214099 atoms, 6729 bonds, 18 pseudobonds, 17854 residues, 4 models selected  

> hide #!61 models

> show #!53 models

> hide #!58 models

> hide #!18 models

Drag select of 440 residues  

> show #!58 models

> show #!18 models

> color zone #18 near sel distance 24

> color single #18

> show #!61 models

> hide #!58 models

> hide #!53 models

> hide #!18 models

> select add #61

418362 atoms, 221714 bonds, 5080 pseudobonds, 35048 residues, 7 models
selected  

> select subtract #61

211296 atoms, 11 pseudobonds, 17445 residues, 3 models selected  
Drag select of 2432 residues, 8 pseudobonds  
Drag select of 777 residues  
Drag select of 3298 residues, 2 pseudobonds  

> select (sel & #61/eEF2)

4941 atoms, 5030 bonds, 637 residues, 1 model selected  

> hide #!61 models

> show #!58 models

Drag select of 17005 residues, 11 pseudobonds  

> hide #!58 models

> show #!52 models

> hide #!52 models

> show #!53 models

Drag select of 440 residues  

> show #!58 models

> show #!61 models

> show #!18 models

> color zone #18 near sel distance 24

> volume splitbyzone #18

Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 0 as #37.1, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 1 as #37.2, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 2 as #37.3, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 3 as #37.4, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 4 as #37.5, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 5 as #37.6, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_cEF2_IF5.mrc 6 as #37.7, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!37 models

> show #!19 models

> hide #!61 models

> select add #61

418362 atoms, 221714 bonds, 5080 pseudobonds, 35048 residues, 7 models
selected  

> select subtract #61

211296 atoms, 11 pseudobonds, 17445 residues, 3 models selected  

> color zone #19 near sel distance 24

> volume splitbyzone #19

Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 0 as #38.1, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 1 as #38.2, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 2 as #38.3, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 3 as #38.4, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 4 as #38.5, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnrotatedPre_none_IF5.mrc 5 as #38.6, grid
size 128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!38 models

> select add #53

412454 atoms, 220182 bonds, 5241 pseudobonds, 33903 residues, 6 models
selected  

> select add #58

414098 atoms, 444901 bonds, 9743 pseudobonds, 33980 residues, 7 models
selected  

> select subtract #58

204962 atoms, 220182 bonds, 5230 pseudobonds, 16898 residues, 4 models
selected  

> select subtract #53

Nothing selected  

> hide #!53 models

> hide #!58 models

> show #!38 models

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/Manuscript1/202512_subunitcolouring.cxs
> includeMaps true

> show #!20 models

> show #!21 models

> show #!22 models

> show #!23 models

> show #!24 models

> show #!25 models

> show #!26 models

> hide #!26 models

> show #!26 models

> show #!27 models

> show #!28 models

> show #!29 models

> show #!30 models

> show #!31 models

> show #!32 models

> show #!33 models

> show #!34 models

> show #!35 models

> show #!36 models

> show #!37 models

> surface dust #20.1 size 40

> surface dust #20.2 size 40

> surface dust #20.3 size 40

> surface dust #20.4 size 40

> surface dust #20.5 size 40

> surface dust #20.6 size 40

> surface dust #20.7 size 40

> surface dust #21.2 size 40

> surface dust #21.3 size 40

> surface dust #21.4 size 40

> surface dust #21.5 size 40

> surface dust #21.6 size 40

> surface dust #21.7 size 40

> surface dust #22.1 size 40

> surface dust #22.2 size 40

> surface dust #22.3 size 40

> surface dust #22.4 size 40

> surface dust #22.5 size 40

> surface dust #22.6 size 40

> surface dust #23.1 size 40

> surface dust #23.2 size 40

> surface dust #23.3 size 40

> surface dust #23.4 size 40

> surface dust #23.5 size 40

> surface dust #23.6 size 40

> surface dust #23.7 size 40

> surface dust #24.1 size 40

> surface dust #24.2 size 40

> surface dust #24.3 size 40

> surface dust #24.4 size 40

> surface dust #24.5 size 40

> surface dust #24.6 size 40

> surface dust #24.7 size 40

> surface dust #25.1 size 40

> surface dust #25.2 size 40

> surface dust #25.3 size 40

> surface dust #25.4 size 40

> surface dust #25.5 size 40

> surface dust #25.6 size 40

> surface dust #26.1 size 40

> surface dust #26.2 size 40

> surface dust #26.3 size 40

> surface dust #26.4 size 40

> surface dust #26.5 size 40

> surface dust #27.1 size 40

> surface dust #27.2 size 40

> surface dust #27.3 size 40

> surface dust #27.4 size 40

> surface dust #27.5 size 40

> surface dust #28.1 size 40

> surface dust #28.2 size 40

> surface dust #28.3 size 40

> surface dust #28.4 size 40

> surface dust #29.1 size 40

> surface dust #29.2 size 40

> surface dust #29.3 size 40

> surface dust #29.4 size 40

> surface dust #29.5 size 40

> surface dust #30.1 size 40

> surface dust #30.2 size 40

> surface dust #30.3 size 40

> surface dust #30.4 size 40

> surface dust #30.5 size 40

> surface dust #31.1 size 40

> surface dust #31.2 size 40

> surface dust #31.3 size 40

> surface dust #31.4 size 40

> surface dust #32.1 size 40

> surface dust #32.2 size 40

> surface dust #32.3 size 40

> surface dust #32.4 size 40

> surface dust #32.5 size 40

> surface dust #33.1 size 40

> surface dust #33.2 size 40

> surface dust #33.3 size 40

> surface dust #33.4 size 40

> surface dust #33.5 size 40

> surface dust #33.6 size 40

> surface dust #33.7 size 40

> surface dust #34.1 size 40

> surface dust #34.2 size 40

> surface dust #34.3 size 40

> surface dust #34.4 size 40

> surface dust #34.5 size 40

> surface dust #34.6 size 40

> surface dust #34.7 size 40

> surface dust #35.1 size 40

> surface dust #35.2 size 40

> surface dust #35.3 size 40

> surface dust #35.4 size 40

> surface dust #35.5 size 40

> surface dust #35.6 size 40

> surface dust #35.7 size 40

> surface dust #36.1 size 40

> surface dust #36.2 size 40

> surface dust #36.3 size 40

> surface dust #36.4 size 40

> surface dust #36.5 size 40

> surface dust #36.6 size 40

> surface dust #37.1 size 40

> surface dust #37.2 size 40

> surface dust #37.3 size 40

> surface dust #37.4 size 40

> surface dust #37.5 size 40

> surface dust #37.6 size 40

> surface dust #37.7 size 40

> surface dust #38.1 size 40

> surface dust #38.2 size 40

> surface dust #38.3 size 40

> surface dust #38.4 size 40

> surface dust #38.5 size 40

> surface dust #38.6 size 40

> hide #!38 models

> hide #!37 models

> hide #!35 models

> hide #!34 models

> hide #!33 models

> hide #!31 models

> hide #!32 models

> hide #!30 models

> hide #!29 models

> hide #!28 models

> hide #!27 models

> hide #!26 models

> hide #!25 models

> hide #!24 models

> hide #!23 models

> hide #!22 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> hide #!36 models

> show #!37 models

> hide #!37 models

> show #!38 models

> show #!37 models

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/Manuscript1/202512_subunitcolouring.cxs
> includeMaps true

——— End of log from Wed Dec 17 16:42:20 2025 ———

> view name session-start

opened ChimeraX session  

> hide #!38 models

> hide #!37 models

> show #!38 models

> hide #!38 models

> show #!33 models

> show #!32 models

> hide #!33 models

> hide #!32 models

> show #!33 models

> hide #!33 models

> show #!20 models

> select add #20

15 models selected  

> select subtract #20

Nothing selected  

> hide #!20 models

> show #!23 models

> show #!24 models

> hide #!23 models

> hide #!24 models

> show #!20 models

> hide #!20 models

> show #!23 models

> hide #!23 models

> show #!24 models

> hide #!24.7 models

> show #!24.7 models

> select add #24

15 models selected  

> hide #!24.7 models

> show #!24.7 models

> hide #!24 models

> show #!24 models

> select subtract #24

Nothing selected  

> hide #!24.6 models

> hide #!24.5 models

> hide #!24.4 models

> hide #!24.3 models

> hide #!24.2 models

> hide #!24.1 models

> hide #!24.7 models

> show #!24.7 models

> hide #!24.7 models

> show #!24.7 models

> show #!5 models

> hide #!5 models

> hide #!24 models

> surface undust all

> show #!24 models

> show #!24.2 models

> show #!24.3 models

> show #!24.4 models

> show #!24.5 models

> show #!24.6 models

> show #!33 models

> hide #!24 models

> show #!61 models

> hide #!61 models

> show #!51 models

> hide #!33 models

> show #!61 models

> show #!59 models

> hide #!61 models

> select add #59

207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models
selected  

> show sel atoms

> undo

> select subtract #59

Nothing selected  

> select add #51

219683 atoms, 235777 bonds, 3975 pseudobonds, 17946 residues, 4 models
selected  

> show sel atoms

> undo

> select subtract #51

Nothing selected  

> show #!14 models

> hide #!14 models

> show #!14 models

> show #!24 models

> hide #!24 models

> hide #!51 models

> show #!51 models

> show #!61 models

> hide #!14 models

> hide #!59 models

> hide #!51 models

> show #!51 models

> hide #!61 models

> show #!61 models

> select clear

Drag select of 3625 residues, 12 pseudobonds  

> hide #!51 models

> show #!14 models

Drag select of 4459 residues, 14 pseudobonds, 14
MultiPostProcessor_PPout_Rotated2.mrc  

> hide #!14 models

> show #!51 models

> show #!14 models

> select subtract #14

51621 atoms, 14 pseudobonds, 4459 residues, 2 models selected  

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

Drag select of 4110 residues, 12 pseudobonds, 14
MultiPostProcessor_PPout_Rotated2.mrc  

> select subtract #14

46106 atoms, 12 pseudobonds, 4110 residues, 3 models selected  

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> select sel & #61/eEF2

6074 atoms, 6181 bonds, 782 residues, 1 model selected  

> hide #!14 models

> hide #!51 models

> show #!51 models

> hide #!61 models

> show #!59 models

Drag select of 17213 residues, 12 pseudobonds  

> show #!61 models

> hide #!61 models

> ui tool show "Color Zone"

> color zone #50 near #59 distance 4

> show #!14 models

> color zone #14 near sel distance 24

> close #33

> volume splitbyzone #14

Opened MultiPostProcessor_PPout_Rotated2.mrc 0 as #33.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 1 as #33.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 2 as #33.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 3 as #33.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 4 as #33.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated2.mrc 5 as #33.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!33.1 models

> select clear

> show #!33.1 models

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/Manuscript1/202512_subunitcolouring.cxs
> includeMaps true

——— End of log from Wed Jan 7 10:53:50 2026 ———

> view name session-start

opened ChimeraX session  

> show #!58 models

> hide #!59 models

> hide #!58 models

> show #!58 models

> show #!59 models

> select #58 color=20B2AA

Expected a keyword  

> select color=20B2AA

Expected an objects specifier or a keyword  

> @/color=20B2AA

Unknown command: @/color=20B2AA  

> select @/color=20B2AA

Expected an objects specifier or a keyword  

> select ssu

362373 atoms, 396658 bonds, 12006 pseudobonds, 23927 residues, 14 models
selected  

> show #!61 models

> show #!60 models

> hide #!60 models

> select ssu

362373 atoms, 396658 bonds, 12006 pseudobonds, 23927 residues, 14 models
selected  

> hide #!58 models

> hide #!59 models

> hide #!61 models

> show #!59 models

> hide #!59 models

> show #!58 models

> hide #!58 models

> show #!60 models

> select clear

> select ssu

362373 atoms, 396658 bonds, 12006 pseudobonds, 23927 residues, 14 models
selected  

> close #1-38#33.1-6

> close #60

> hide #!51 models

> show #!50 models

> show #!58 models

> show #!59 models

> show #!61 models

> hide #!50 models

> hide #!59 models

> show #!59 models

> hide #!59 models

> hide #!61 models

> hide #!58 models

> show #!59 models

> hide #!59 models

> show #!61 models

> log metadata #51

No models had metadata

> log chains #51

Chain information for A/P, P/E #51  
---  
Chain | Description | UniProt  
1 | nascent chain |   
33 | P/E tRNA |   
51 | 28S ribosomal RNA |   
71 | 5S ribosomal RNA |   
81 | 5.8S ribosomal RNA |   
A2 | 18S ribosomal RNA |   
A3 | Ribosomal protein L8 | G1TT27_RABIT 1-257  
B2 | uS2 |   
B3 | uL3 | G1TL06_RABIT 2-403  
C2 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264  
C3 | uL4 |   
D2 | uS5 |   
D3 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297  
E2 | uS3 | G1TNM3_RABIT 1-243  
E3 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291  
F2 | eS4 |   
F3 | uL30 | G1TUB1_RABIT 1-247  
G2 | Ribosomal protein S5 | G1TFM5_RABIT 1-204  
G3 | eL8 |   
H2 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249  
H3 | uL6 | G1TX33_RABIT 1-192  
I2 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194  
I3 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214  
J2 | eS8 |   
J3 | Ribosomal protein L11 | G1TUB8_RABIT 1-178  
K2 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194  
L2 | eS10 | G1TPV3_RABIT 1-165  
L3 | eL13 |   
M2 | Ribosomal protein S11 | G1TRM4_RABIT 1-158  
M3 | Ribosomal protein L14 | G1SZ12_RABIT 1-218  
N2 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132  
N3 | Ribosomal protein L15 | G1T0C1_RABIT 1-204  
O2 | uS15 | G1SP51_RABIT 1-151  
O3 | uL13 |   
P2 | uS11 |   
P3 | uL22 | G1TVT6_RABIT 1-184  
Q2 | uS19 | G1U0Q2_RABIT 1-145  
Q3 | eL18 |   
R2 | Ribosomal protein S16 | G1SGX4_RABIT 1-146  
R3 | eL19 |   
S2 | eS17 | G1TU13_RABIT 1-135  
S3 | eL20 |   
T2 | uS13 | G1TPG3_RABIT 1-152  
T3 | eL21 | G1SHQ2_RABIT 1-160  
U2 | eS19 |   
U3 | eL22 |   
V2 | uS10 | G1SIZ2_RABIT 1-119  
V3 | Ribosomal protein L23 | G1T6D1_RABIT 1-140  
W2 | eS21 |   
X2 | Ribosomal protein S15a | G1TG89_RABIT 1-130  
X3 | uL23 | G1SE76_RABIT 1-156  
Y2 | uS12 |   
Y3 | Ribosomal protein L26 | G1SQH0_RABIT 1-145  
Z2 | eS24 |   
Z3 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136  
a2 | eS25 | G1TDB3_RABIT 1-125  
a3 | uL15 | G1SNY0_RABIT 2-148  
b2 | eS26 |   
b3 | eL29 | G1SGR6_RABIT 1-226  
c2 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84  
c3 | eL30 | G1TDL2_RABIT 1-115  
d2 | Ribosomal protein S28 | G1TIB4_RABIT 1-69  
d3 | eL31 | G1SHG0_RABIT 1-125  
e2 | uS14 | G1U7M4_RABIT 1-56  
e3 | eL32 | G1U437_RABIT 1-135  
f2 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132  
f3 | eL33 | G1SF08_RABIT 1-110  
g2 | Ribosomal protein S27a | G1SK22_RABIT 1-156  
g3 | eL34 |   
h2 | RACK1 | G1SJB4_RABIT 1-317  
h3 | uL29 | G1SIT5_RABIT 1-123  
i3 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105  
j3 | Ribosomal protein L37 | U3KPD5_RABIT 1-97  
k3 | eL38 |   
l3 | eL39 | G1TTN1_RABIT 1-51  
m3 | eL40 |   
n3 | eL41 |   
o3 | eL42 |   
p3 | eL43 | G1SY53_RABIT 1-92  
q3 | A/P RNA |   
r3 | eL28 | G1U7L1_RABIT 1-137  
t3 | uL10 |   
u3 | Ribosomal protein L12 | G1SMR7_RABIT 1-165  
v3 | mRNA |   
w3 | uL1 | G1SKZ8_RABIT 1-217  
  

> log metadata #52

No models had metadata

> log chains #52

Chain information for EF1, A/T, P, E #52  
---  
Chain | Description | UniProt  
2 ii | tRNA |   
3 | E-site tRNA |   
5 | 28S ribosomal RNA |   
7 | 5S ribosomal RNA |   
8 | 5.8S ribosomal RNA |   
9 | 18S ribosomal RNA |   
A | uL2 | G1TT27_RABIT 1-257  
AA | uS2 |   
B | uL3 | G1TL06_RABIT 2-403  
BB | 40S ribosomal protein S3a | G1SS70_RABIT 1-264  
C | uL4 | G1SVW5_RABIT 1-378  
CC | uS5 |   
D | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297  
DD | uS4 | G1TNM3_RABIT 1-243  
E | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291  
EE | 40S ribosomal protein S4 |   
F | uL30 | G1TUB1_RABIT 1-247  
FF | Uncharacterized protein | G1TFM5_RABIT 1-204  
G | eL8 | G1STW0_RABIT 78-319  
GG | 40S ribosomal protein S6 | G1TM55_RABIT 1-249  
H | uL6 | G1TX33_RABIT 1-192  
HH | uS7 | G1SVB0_RABIT 1-194  
I | Ribosomal protein L10 (Predicted) | B7NZQ2_RABIT 1-214  
II | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208  
J | uL5 | G1TUB8_RABIT 1-178  
JJ | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194  
KK | eS10 | G1TPV3_RABIT 1-165  
L | eL13 |   
LL | uS17 | G1TRM4_RABIT 1-158  
M | eL14 | G1SZ12_RABIT 1-218  
MM | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132  
N | Ribosomal protein L15 | G1T0C1_RABIT 1-204  
NN | uS15 | G1SP51_RABIT 1-151  
O | uL13 |   
OO | uS11 | G1T1F0_RABIT -4-151  
P | uL22 | G1TVT6_RABIT 1-184  
PP | uS19 | G1U0Q2_RABIT 1-145  
Q | eL18 |   
QQ | uS9 | G1SGX4_RABIT 1-146  
R | eL19 |   
RR | eS17 | G1TU13_RABIT 1-135  
S | eL20 |   
SS | uS13 | G1TPG3_RABIT 1-152  
T | eL21 | G1SHQ2_RABIT 1-160  
TT | eS19 | G1TN62_RABIT 1-145  
U | eL22 |   
UU | uS10 | G1SIZ2_RABIT 1-119  
V | uL14 | G1T6D1_RABIT 1-140  
VV | eS21 |   
W | uL24 | G1SE28_RABIT 1-157  
WW | uS8 | G1TG89_RABIT 1-130  
X | uL23 | G1SE76_RABIT 1-156  
XX | uS12 |   
Y | uL24 | G1SQH0_RABIT 1-145  
YY | eS24 |   
Z | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136  
ZZ | eS25 | G1TDB3_RABIT 1-125  
a | uL15 | G1SNY0_RABIT 1-148  
aa | eS26 |   
b | eL29 | G1SGR6_RABIT 1-226  
bb | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84  
c | eL30 | G1TDL2_RABIT 1-115  
cc | eS28 | G1TIB4_RABIT 1-69  
d | eL31 | G1SHG0_RABIT 1-125  
dd | uS14 | G1U7M4_RABIT 1-56  
e | eL32 | G1U437_RABIT 1-135  
ee | eS30 | G1T8A2_RABIT 0-132  
f | eL33 | G1SF08_RABIT 1-110  
ff | eS31 | G1SK22_RABIT 1-156  
g | eL34 | G1U945_RABIT 1-116  
gg | RACK1 | G1SJB4_RABIT 1-317  
h | uL29 | G1SIT5_RABIT 1-123  
hh | mRNA |   
i | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105  
j | Ribosomal protein L37 | U3KPD5_RABIT 1-97  
jj | Elongation factor 1-alpha 1 | EF1A1_RABIT 1-462  
k | eL38 |   
l | eL39 | G1TTN1_RABIT 1-51  
m | eL40 |   
n | 60s ribosomal protein l41 |   
o | eL42 | G1U344_RABIT 1-106  
p | eL43 | G1SY53_RABIT 1-92  
r | eL28 | G1U7L1_RABIT 1-137  
s | uL10 |   
t | uL11 | G1SMR7_RABIT 1-165  
  

> log metadata #53

No models had metadata

> log chains #53

Chain information for A, IF5 and L-contact #53  
---  
Chain | Description | UniProt  
2 | 18S rRNA |   
A | 40S ribosomal protein S3 | RS3_YEAST 4-225  
AA | 60S ribosomal protein L8-A | RL8A_YEAST 24-256  
AB | 60S ribosomal protein L23-A | RL23A_YEAST 2-137  
AC | 60S ribosomal protein L36-A | RL36A_YEAST 2-100  
AD | 60S ribosomal protein L9-A | RL9A_YEAST 1-191  
AE | 60S ribosomal protein L24-A | RL24A_YEAST 1-126  
AF | 60S ribosomal protein L37-A | RL37A_YEAST 2-82  
AG | 60S ribosomal protein L11-B | RL11B_YEAST 6-174  
AH | 60S ribosomal protein L25 | RL25_YEAST 22-142  
AI | 60S ribosomal protein L38 | RL38_YEAST 2-78  
AJ | 60S ribosomal protein L13-A | RL13A_YEAST 2-194  
AK | 60S ribosomal protein L26-A | RL26A_YEAST 2-126  
AL | 60S ribosomal protein L39 | RL39_YEAST 2-51  
AM | 60S ribosomal protein L14-A | RL14A_YEAST 3-138  
AN | 60S ribosomal protein L27-A | RL27A_YEAST 2-136  
AO | Ubiquitin-60S ribosomal protein L40 | RL40A_YEAST 77-128  
AP | 60S ribosomal protein L42-A | RL44A_YEAST 2-104  
AQ | 60S ribosomal protein L15-A | RL15A_YEAST 2-204  
AR | 60S ribosomal protein L28 | RL28_YEAST 2-149  
AS | 60S ribosomal protein L41-A |   
AT | 60S ribosomal protein L43-A | RL43A_YEAST 2-92  
AU | 60S ribosomal protein L16-A | RL16A_YEAST 3-199  
AV | 60S ribosomal protein L29 | RL29_YEAST 2-59  
AW | 60S ribosomal protein L2-A | RL2A_YEAST 2-252  
AX | 60S ribosomal protein L17-A | RL17A_YEAST 2-184  
AY | 60S ribosomal protein L30 | RL30_YEAST 9-104  
B | Rps5p | A0A1L4AA68_YEASX 20-225  
BA | 60S ribosomal protein L3 | RL3_YEAST 2-387  
BB | 60S ribosomal protein L18-A | RL18A_YEAST 2-186  
BC | 60S ribosomal protein L31-A | RL31A_YEAST 4-112  
BD | 60S ribosomal protein L10 | RL10_YEAST 2-219  
BE | 60S ribosomal protein L4-A | RL4A_YEAST 2-362  
BF | 60S ribosomal protein L19-A | RL19A_YEAST 2-189  
BG | 60S ribosomal protein L32 | RL32_YEAST 2-128  
BH | 60S ribosomal protein L20-A | RL20A_YEAST 2-172  
BI | 60S ribosomal protein L5 | RL5_YEAST 4-297  
BJ | 60S ribosomal protein L21-A | RL21A_YEAST 2-160  
BK | 60S ribosomal protein L33-A | RL33A_YEAST 2-107  
BL | 60S ribosomal protein L22-A | RL22A_YEAST 9-108  
BM | 60S ribosomal protein L6-B | RL6B_YEAST 2-176  
BN | 60S ribosomal protein L34-A | RL34A_YEAST 2-113  
BO | 60S ribosomal protein L7-A | RL7A_YEAST 23-244  
BP | 60S ribosomal protein L35-A | RL35A_YEAST 2-120  
BQ | 25S rRNA |   
BR | 5S rRNA |   
BS | 5.8S rRNA |   
BT | 60S ribosomal protein L1 |   
C | 40S ribosomal protein S10-A | RS10A_YEAST 1-92  
D | 40S ribosomal protein S12 | RS12_YEAST 23-143  
E | 40S ribosomal protein S15 | RS15_YEAST 13-129  
F | 40S ribosomal protein S16-A | RS16A_YEAST 3-143  
G | 40S ribosomal protein S17-B | RS17B_YEAST 2-126  
H | 40S ribosomal protein S18-A | RS18A_YEAST 2-146  
I | 40S ribosomal protein S19-A | RS19A_YEAST 2-144  
J | 40S ribosomal protein S20 | RS20_YEAST 20-119  
K | 40S ribosomal protein S25-A | RS25A_YEAST 24-105  
L | 40S ribosomal protein S28-A | RS28A_YEAST 5-67  
M | 40S ribosomal protein S29-A | RS29A_YEAST 4-56  
N | Ubiquitin-40S ribosomal protein S31 | RS31_YEAST 80-152  
O | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 5-316  
P | 40S ribosomal protein S0-A | RSSA1_YEAS1 2-207  
Q | 40S ribosomal protein S1-A | RS3A1_YEAS1 2-233  
R | 40S ribosomal protein S2 | RS2_YEAST 34-249  
S | 40S ribosomal protein S4-A | RS4A_YEAST 2-259  
T | 40S ribosomal protein S6-A | RS6A_YEAST 1-228  
U | 40S ribosomal protein S7-A | RS7A_YEAST 4-187  
V | 40S ribosomal protein S8 | A0A0J9X221_LACKL 2-199  
W | 40S ribosomal protein S9-A | RS9A_YEAST 2-185  
X | 40S ribosomal protein S11-A | RS11A_YEAST 4-145  
Y | 40S ribosomal protein S13 | RS13_YEAST 2-151  
Z | 40S ribosomal protein S14-B | RS14B_YEAST 11-137  
a | 40S ribosomal protein S21-A | RS21A_YEAST 1-87  
b | 40S ribosomal protein S22-A | RS22A_YEAST 2-130  
c | 40S ribosomal protein S23-A | RS23A_YEAST 2-145  
d | 40S ribosomal protein S24-A | RS24A_YEAST 2-135  
e | 40S ribosomal protein S26-B | RS26B_YEAST 2-98  
eI | Eukaryotic translation initiation factor 5A-1 | IF5A1_YEAST 4-157  
f | 40S ribosomal protein S27-A | RS27A_YEAST 2-82  
g | 40S ribosomal protein S30-A | RS30A_YEAST 2-61  
l | mRNA |   
m | A-site tRNA |   
n | P-site tRNA |   
  

> log metadata #58

No models had metadata

> log chains #58

Chain information for Unrotated base, P #58  
---  
Chain | Description | UniProt  
10 | 40S ribosomal protein S10 | RS10A_YEAST 1-105  
11 | 40S ribosomal protein S11 | RS11A_YEAST 1-156  
12 | 40S ribosomal protein S12 | RS12_YEAST 1-143  
13 | 40S ribosomal protein S13 | RS13_YEAST 1-151  
14 | 40S ribosomal protein S14 | RS14A_YEAST 1-137  
15 | 40S ribosomal protein S15 | RS15_YEAST 1-142  
16 | 40S ribosomal protein S16 | RS16A_YEAST 1-143  
17 | 40S ribosomal protein S17 | RS17A_YEAST 1-136  
18 | 40S ribosomal protein S18 | RS18A_YEAST 1-146  
19 | 40S ribosomal protein S19 | RS19A_YEAST 1-144  
1S | 18S ribosomal RNA |   
20 | 40S ribosomal protein S20 | RS20_YEAST 1-121  
21 | 40S ribosomal protein S21 | RS21A_YEAST 1-87  
22 | 40S ribosomal protein S22 | RS22A_YEAST 1-130  
23 | 40S ribosomal protein S23 | RS23A_YEAST 1-145  
24 | 40S ribosomal protein S24 | RS24A_YEAST 1-135  
25 | 40S ribosomal protein S25 | RS25A_YEAST 1-108  
26 | 40S ribosomal protein S26 | RS26A_YEAST 1-119  
27 | 40S ribosomal protein S27 | RS27_YEAST 1-82  
28 | 40S ribosomal protein S28 | RS28A_YEAST 1-67  
29 | 40S ribosomal protein S29 | RS29A_YEAST 1-56  
2S | 25S ribosomal RNA |   
30 | 40S ribosomal protein S30 | RS30A_YEAST 1-63  
31 | 40S ribosomal protein S31 | RS27A_YEAST 1-152  
5S | 5S ribosomal RNA |   
60 | 60S ribosomal protein L10 | RL10_YEAST 1-221  
61 | 60S ribosomal protein L11 | RL11A_YEAST 1-174  
62 | 60S ribosomal protein L12 | RL12A_YEAST 1-165  
63 | 60S ribosomal protein L13 | RL13A_YEAST 1-199  
64 | 60S ribosomal protein L14 | RL14A_YEAST 1-138  
65 | 60S ribosomal protein L15 | RL15A_YEAST 1-204  
66 | 60S ribosomal protein L16 | RL16A_YEAST 1-199  
67 | 60S ribosomal protein L17 | RL17A_YEAST 1-184  
68 | 60S ribosomal protein L18 | RL18A_YEAST 1-186  
69 | 60S ribosomal protein L19 | RL19A_YEAST 1-189  
70 | 60S ribosomal protein L20 | RL20A_YEAST 1-172  
71 | 60S ribosomal protein L21 | RL21A_YEAST 1-160  
72 | 60S ribosomal protein L22 | RL22A_YEAST 1-121  
73 | 60S ribosomal protein L23 | RL23A_YEAST 1-137  
74 | 60S ribosomal protein L24 | RL24A_YEAST 1-155  
75 | 60S ribosomal protein L25 | RL25_YEAST 1-142  
76 | 60S ribosomal protein L26 | RL26A_YEAST 1-127  
77 | 60S ribosomal protein L27 | RL27A_YEAST 1-136  
78 | 60S ribosomal protein L28 | RL28_YEAST 1-149  
79 | 60S ribosomal protein L29 | RL29_YEAST 1-59  
80 | 60S ribosomal protein L30 | RL30_YEAST 1-105  
81 | 60S ribosomal protein L31 | RL31A_YEAST 1-113  
82 | 60S ribosomal protein L32 | RL32_YEAST 1-130  
83 | 60S ribosomal protein L33 | RL33A_YEAST 1-107  
84 | 60S ribosomal protein L34 | RL34A_YEAST 1-121  
85 | 60S ribosomal protein L35 | RL35A_YEAST 1-120  
86 | 60S ribosomal protein L36 | RL36A_YEAST 1-100  
87 | 60S ribosomal protein L37 | RL37A_YEAST 1-88  
88 | 60S ribosomal protein L38 | RL38_YEAST 1-78  
89 | 60S ribosomal protein L39 | RL39_YEAST 1-51  
8S | 5.8S ribosomal RNA |   
90 | 60S ribosomal protein L40 | RL401_YEAST 1-128  
91 | 60S ribosomal protein L41 | RL41A_YEAST 1-25  
92 | 60S ribosomal protein L42 | RL44A_YEAST 1-106  
93 | 60S ribosomal protein L43 | RL43A_YEAST 1-92  
ET PT | P/E-site initiator transfer RNAfMet |   
L1 | 60S ribosomal protein L1 | RL1A_YEAST 1-217  
L2 | 60S ribosomal protein L2 | RL2A_YEAST 1-254  
L3 | 60S ribosomal protein L3 | RL3_YEAST 1-387  
L4 | 60S ribosomal protein L4 | RL4A_YEAST 1-362  
L5 | 60S ribosomal protein L5 | RL5_YEAST 1-297  
L6 | 60S ribosomal protein L6 | RL6A_YEAST 1-176  
L7 | 60S ribosomal protein L7 | RL7A_YEAST 1-244  
L8 | 60S ribosomal protein L8 | RL8A_YEAST 1-256  
L9 | 60S ribosomal protein L9 | RL9A_YEAST 1-191  
MR | messenger RNA |   
P0 | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-312  
RC | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 1-319  
S0 | 40S ribosomal protein S0 | RSSA1_YEAST 1-252  
S1 | 40S ribosomal protein S1 | RS3A1_YEAST 1-255  
S2 | 40S ribosomal protein S2 | RS2_YEAST 1-254  
S3 | 40S ribosomal protein S3 | RS3_YEAST 1-240  
S4 | 40S ribosomal protein S4 | RS4A_YEAST 1-261  
S5 | 40S ribosomal protein S5 | RS5_YEAST 1-225  
S6 | 40S ribosomal protein S6 | RS6A_YEAST 1-236  
S7 | 40S ribosomal protein S7 | RS7A_YEAST 1-190  
S8 | 40S ribosomal protein S8 | RS8A_YEAST 1-200  
S9 | 40S ribosomal protein S9 | RS9A_YEAST 1-197  
  

> log metadata #59

No models had metadata

> log chains #59

Chain information for Rotated base #59  
---  
Chain | Description | UniProt  
10 | 40S ribosomal protein S10 | RS10A_YEAST 1-105  
11 | 40S ribosomal protein S11 | RS11A_YEAST 1-156  
12 | 40S ribosomal protein S12 | RS12_YEAST 1-143  
13 | 40S ribosomal protein S13 | RS13_YEAST 1-151  
14 | 40S ribosomal protein S14 | RS14A_YEAST 1-137  
15 | 40S ribosomal protein S15 | RS15_YEAST 1-142  
16 | 40S ribosomal protein S16 | RS16A_YEAST 1-143  
17 | 40S ribosomal protein S17 | RS17A_YEAST 1-136  
18 | 40S ribosomal protein S18 | RS18A_YEAST 1-146  
19 | 40S ribosomal protein S19 | RS19A_YEAST 1-144  
1S | 18S ribosomal RNA |   
20 | 40S ribosomal protein S20 | RS20_YEAST 1-121  
21 | 40S ribosomal protein S21 | RS21A_YEAST 1-87  
22 | 40S ribosomal protein S22 | RS22A_YEAST 1-130  
23 | 40S ribosomal protein S23 | RS23A_YEAST 1-145  
24 | 40S ribosomal protein S24 | RS24A_YEAST 1-135  
25 | 40S ribosomal protein S25 | RS25A_YEAST 1-108  
26 | 40S ribosomal protein S26 | RS26A_YEAST 1-119  
27 | 40S ribosomal protein S27 | RS27_YEAST 1-82  
28 | 40S ribosomal protein S28 | RS28A_YEAST 1-67  
29 | 40S ribosomal protein S29 | RS29A_YEAST 1-56  
2S | 25S ribosomal RNA |   
30 | 40S ribosomal protein S30 | RS30A_YEAST 1-63  
31 | 40S ribosomal protein S31 | RS27A_YEAST 1-152  
5S | 5S ribosomal RNA |   
60 | 60S ribosomal protein L10 | RL10_YEAST 1-221  
61 | 60S ribosomal protein L11 | RL11A_YEAST 1-174  
62 | 60S ribosomal protein L12 | RL12A_YEAST 1-165  
63 | 60S ribosomal protein L13 | RL13A_YEAST 1-199  
64 | 60S ribosomal protein L14 | RL14A_YEAST 1-138  
65 | 60S ribosomal protein L15 | RL15A_YEAST 1-204  
66 | 60S ribosomal protein L16 | RL16A_YEAST 1-199  
67 | 60S ribosomal protein L17 | RL17A_YEAST 1-184  
68 | 60S ribosomal protein L18 | RL18A_YEAST 1-186  
69 | 60S ribosomal protein L19 | RL19A_YEAST 1-189  
70 | 60S ribosomal protein L20 | RL20A_YEAST 1-172  
71 | 60S ribosomal protein L21 | RL21A_YEAST 1-160  
72 | 60S ribosomal protein L22 | RL22A_YEAST 1-121  
73 | 60S ribosomal protein L23 | RL23A_YEAST 1-137  
74 | 60S ribosomal protein L24 | RL24A_YEAST 1-155  
75 | 60S ribosomal protein L25 | RL25_YEAST 1-142  
76 | 60S ribosomal protein L26 | RL26A_YEAST 1-127  
77 | 60S ribosomal protein L27 | RL27A_YEAST 1-136  
78 | 60S ribosomal protein L28 | RL28_YEAST 1-149  
79 | 60S ribosomal protein L29 | RL29_YEAST 1-59  
80 | 60S ribosomal protein L30 | RL30_YEAST 1-105  
81 | 60S ribosomal protein L31 | RL31A_YEAST 1-113  
82 | 60S ribosomal protein L32 | RL32_YEAST 1-130  
83 | 60S ribosomal protein L33 | RL33A_YEAST 1-107  
84 | 60S ribosomal protein L34 | RL34A_YEAST 1-121  
85 | 60S ribosomal protein L35 | RL35A_YEAST 1-120  
86 | 60S ribosomal protein L36 | RL36A_YEAST 1-100  
87 | 60S ribosomal protein L37 | RL37A_YEAST 1-88  
88 | 60S ribosomal protein L38 | RL38_YEAST 1-78  
89 | 60S ribosomal protein L39 | RL39_YEAST 1-51  
8S | 5.8S ribosomal RNA |   
90 | 60S ribosomal protein L40 | RL401_YEAST 1-128  
91 | 60S ribosomal protein L41 | RL41A_YEAST 1-25  
92 | 60S ribosomal protein L42 | RL44A_YEAST 1-106  
93 | 60S ribosomal protein L43 | RL43A_YEAST 1-92  
L1 | 60S ribosomal protein L1 | RL1A_YEAST 1-217  
L2 | 60S ribosomal protein L2 | RL2A_YEAST 1-254  
L3 | 60S ribosomal protein L3 | RL3_YEAST 1-387  
L4 | 60S ribosomal protein L4 | RL4A_YEAST 1-362  
L5 | 60S ribosomal protein L5 | RL5_YEAST 1-297  
L6 | 60S ribosomal protein L6 | RL6A_YEAST 1-176  
L7 | 60S ribosomal protein L7 | RL7A_YEAST 1-244  
L8 | 60S ribosomal protein L8 | RL8A_YEAST 1-256  
L9 | 60S ribosomal protein L9 | RL9A_YEAST 1-191  
MR | messenger RNA |   
P0 | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-312  
PT | P/E-site initiator transfer RNAfMet |   
RC | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 1-319  
S0 | 40S ribosomal protein S0 | RSSA1_YEAST 1-252  
S1 | 40S ribosomal protein S1 | RS3A1_YEAST 1-255  
S2 | 40S ribosomal protein S2 | RS2_YEAST 1-254  
S3 | 40S ribosomal protein S3 | RS3_YEAST 1-240  
S4 | 40S ribosomal protein S4 | RS4A_YEAST 1-261  
S5 | 40S ribosomal protein S5 | RS5_YEAST 1-225  
S6 | 40S ribosomal protein S6 | RS6A_YEAST 1-236  
S7 | 40S ribosomal protein S7 | RS7A_YEAST 1-190  
S8 | 40S ribosomal protein S8 | RS8A_YEAST 1-200  
S9 | 40S ribosomal protein S9 | RS9A_YEAST 1-197  
  

> log metadata #61

No models had metadata

> log chains #61

Chain information for Swivel base, eEF2 #61  
---  
Chain | Description | UniProt  
18S | 18S rRNA |   
25S | 25S rRNA |   
58S | 5.8S rRNA |   
AB | 5S rRNA |   
ASIT | PHE tRNA |   
PSIT | FMET tRNA |   
RACK | BJ4_G0022010.mRNA.1.CDS.1 | A0A6L1BKH8_YEASX 1-319  
eEF2 | Elongation factor 2 | A0A6A5Q7K2_YEASX 1-842  
eL13 | 60S ribosomal protein L13 | A0A6L1AF71_YEASX 1-199  
eL14 | 60S ribosomal protein L14-A | RL14A_YEAST 1-138  
eL15 | 60S ribosomal protein L15-A | RL15A_YEAST 1-204  
eL18 | BJ4_G0033900.mRNA.1.CDS.1 | A0A6L1A7F6_YEASX 1-186  
eL19 | 60S ribosomal protein L19-A | RL19A_YEAST 1-189  
eL20 | 60S ribosomal protein L20 | A0A6V8RR03_YEASX 1-172  
eL21 | BJ4_G0003770.mRNA.1.CDS.1 | A0A6L0YTI6_YEASX 1-160  
eL22 | 60S ribosomal protein L22-A | A0A6L0ZZW6_YEASX 1-121  
eL24 | 60S ribosomal protein L24-A | A0A6A5PY83_YEASX 1-155  
eL27 | 60S ribosomal protein L27 | A0A6L0ZQQ7_YEASX 1-136  
eL29 | 60S ribosomal protein L29 | A0A6A5PWR1_YEASX 1-59  
eL30 | BJ4_G0020000.mRNA.1.CDS.1 | A0A6L0ZM08_YEASX 1-105  
eL31 | BJ4_G0008090.mRNA.1.CDS.1 | A0A6L0YFR2_YEASX 1-113  
eL32 | HN1_G0013350.mRNA.1.CDS.1 | A0A7I9CD28_YEASX 1-130  
eL33 | BJ4_G0025510.mRNA.1.CDS.1 | A0A6L1C3H0_YEASX 1-107  
eL34 | 60S ribosomal protein L34-A | A0A6L0ZFW3_YEASX 1-121  
eL36 | 60S ribosomal protein L36-A | RL36A_YEAST 1-100  
eL37 | Ribosomal protein L37 | A0A6L1BIE7_YEASX 1-88  
eL38 | BJ4_G0032190.mRNA.1.CDS.1 | A0A6A5PUL8_YEASX 1-78  
eL39 | 60S ribosomal protein L39 | A0A6L1ASX0_YEASX 1-51  
eL40 | Ubiquitin | A0A6V8S9K0_YEASX 1-128  
eL41 | eL41 |   
eL42 | BJ4_G0001880.mRNA.1.CDS.1 | A0A6L1B5X0_YEASX 1-106  
eL43 | 60S ribosomal protein L43-A | RL43A_YEAST 1-92  
eL6 | 60S ribosomal protein L6 | A0A6L1BLT3_YEASX 1-176  
eL8 | 60S ribosomal protein L8-A | RL8A_YEAST 1-256  
eS1 | 40S ribosomal protein S1 | A0A6A5PRY4_YEASX 1-255  
eS10 | 40S ribosomal protein S10-A | A0A6L0ZM59_YEASX 1-105  
eS17 | BJ4_G0020710.mRNA.1.CDS.1 | A0A6L1BLL7_YEASX 1-136  
eS19 | 40S ribosomal protein S19-A | A0A6L1BWT3_YEASX 1-144  
eS21 | 40S ribosomal protein S21 | A0A6L1BDN3_YEASX 1-87  
eS24 | 40S ribosomal protein S24 | A0A6L1AUB6_YEASX 1-135  
eS25 | 40S ribosomal protein S25 | A0A6A5PZ18_YEASX 1-108  
eS26 | 40S ribosomal protein S26 | A0A6A5PUG0_YEASX 1-119  
eS27 | 40S ribosomal protein S27-A | RS27A_YEAST 1-82  
eS28 | eS28 | A0A6A5Q700_YEASX 1-67  
eS30 | 40S ribosomal protein S30 | A0A6L1A1E1_YEASX 1-63  
eS31 | Ubiquitin-40S ribosomal protein S31 | A0A6A5PU37_YEASX 1-152  
eS4 | 40S ribosomal protein S4 | A0A6L0Z3Q0_YEASX 1-261  
eS6 | 40S ribosomal protein S6 | A0A6L1AMY1_YEASX 1-236  
eS7 | 40S ribosomal protein S7 | A0A6L1ACT7_YEASX 1-190  
eS8 | 40S ribosomal protein S8 | A0A6A5Q1H1_YEASX 1-200  
mRNA | MRNA |   
uL10 | 60S acidic ribosomal protein P0 | A0A6A5PT43_YEASX 1-312  
uL11 | 60S ribosomal protein L12-B | A0A6A5Q275_YEASX 1-165  
uL13 | 60S ribosomal protein L16-A | A0A6L0ZD57_YEASX 1-199  
uL14 | 60S ribosomal protein L23-B | A0A6L0Z7E4_YEASX 1-137  
uL15 | 60S ribosomal protein L28 | A0A6L0ZDK5_YEASX 1-149  
uL16 | 60S ribosomal protein L10 | A0A6A5PUZ5_YEASX 1-221  
uL18 | 60S ribosomal protein L5 | A0A6A5Q0W8_YEASX 1-297  
uL2 | 60S ribosomal protein L2-B | A0A6L0Y8L2_YEASX 1-254  
uL22 | BJ4_G0005750.mRNA.1.CDS.1 | A0A6L1BCL1_YEASX 1-184  
uL23 | 60S ribosomal protein L25 | A0A6L0YSM0_YEASX 1-142  
uL24 | 60S ribosomal protein L26-A | RL26A_YEAST 1-127  
uL29 | BJ4_G0044250.mRNA.1.CDS.1 | A0A7I9BRN0_YEASX 1-120  
uL3 | 60S ribosomal protein L3 | A0A6A5Q627_YEASX 1-387  
uL30 | 60S ribosomal protein L7-A | A0A6V8RJA7_YEASX 1-244  
uL4 | BJ4_G0008850.mRNA.1.CDS.1 | A0A6A5Q3W0_YEASX 1-362  
uL5 | BJ4_G0027750.mRNA.1.CDS.1 | A0A6A5Q7I9_YEASX 1-174  
uL6 | 60S ribosomal protein L9-A | RL9A_YEAST 1-191  
uS10 | 40S ribosomal protein S20 | A0A6A5PVE9_YEASX 1-121  
uS11 | 40S ribosomal protein S14-A | A0A6L1AAG7_YEASX 1-137  
uS12 | 40S ribosomal protein S23 | A0A6L1B1T2_YEASX 1-145  
uS13 | 40S ribosomal protein S18-B | A0A6L1AIT6_YEASX 1-146  
uS14 | HLJ1_G0030400.mRNA.1.CDS.1 | A0A6A5PV92_YEASX 1-56  
uS15 | 40S ribosomal protein S13 | A0A6L0YFM5_YEASX 1-151  
uS17 | 40S ribosomal protein S11-B | A0A6L0YMX6_YEASX 1-156  
uS19 | 40S ribosomal protein S15 | A0A6A5Q6F2_YEASX 1-142  
uS2 | 40S ribosomal protein S0 | A0A6L0ZRP4_YEASX 1-252  
uS3 | BJ4_G0045400.mRNA.1.CDS.1 | A0A6L0ZVK6_YEASX 1-240  
uS4 | BJ4_G0026100.mRNA.1.CDS.1 | A0A7I9GPQ3_YEASX 1-197  
uS5 | 40S ribosomal protein S2 | A0A6A5PWF7_YEASX 1-254  
uS7 | Rps5p | A0A1L4AA68_YEASX 1-225  
uS8 | 40S ribosomal protein S22-A | A0A6A5PSE9_YEASX 1-130  
uS9 | BJ4_G0008010.mRNA.1.CDS.1 | A0A6L0YQ58_YEASX 1-143  
  

> select #61/18S:1-1798

36918 atoms, 41291 bonds, 1375 pseudobonds, 1732 residues, 3 models selected  

> select #61/25S:3-3396

67633 atoms, 75699 bonds, 2772 pseudobonds, 3162 residues, 3 models selected  

> select #61/58S:1-158

3353 atoms, 3746 bonds, 83 pseudobonds, 158 residues, 2 models selected  

> select ssu

257320 atoms, 279588 bonds, 7349 pseudobonds, 18591 residues, 10 models
selected  

> select subtract #61/25S

189370 atoms, 203889 bonds, 4286 pseudobonds, 15112 residues, 10 models
selected  

> select add #61/*S**

296405 atoms, 319951 bonds, 7680 pseudobonds, 23042 residues, 10 models
selected  

> select subtract #61/25S

228455 atoms, 244252 bonds, 4496 pseudobonds, 19563 residues, 10 models
selected  

> select subtract #61/58S

225095 atoms, 240506 bonds, 4410 pseudobonds, 19398 residues, 10 models
selected  

> select add #61/RACK

227531 atoms, 242995 bonds, 4410 pseudobonds, 19716 residues, 10 models
selected  

> name frozen ssu sel

> select ~sel & ##selected

396422 atoms, 426545 bonds, 9600 pseudobonds, 32033 residues, 10 models
selected  

> select ssu

227531 atoms, 242995 bonds, 4410 pseudobonds, 19716 residues, 10 models
selected  

> select #61/eS6:195

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

> select up

293 atoms, 294 bonds, 35 residues, 1 model selected  

> select up

1766 atoms, 1790 bonds, 219 residues, 1 model selected  

> select up

1768 atoms, 1790 bonds, 221 residues, 1 model selected  

> select clear

> show #!59 models

> show #!58 models

> select add #58

209136 atoms, 224719 bonds, 4513 pseudobonds, 17082 residues, 3 models
selected  

> select add #59

416887 atoms, 447826 bonds, 8941 pseudobonds, 34146 residues, 6 models
selected  

> select add #61

623953 atoms, 669540 bonds, 14010 pseudobonds, 51749 residues, 10 models
selected  

> show sel cartoons

> select clear

> select ssu

227531 atoms, 242995 bonds, 4410 pseudobonds, 19716 residues, 10 models
selected  

> select ~sel & ##selected

396422 atoms, 426545 bonds, 9600 pseudobonds, 32033 residues, 10 models
selected  

> select ssu

227531 atoms, 242995 bonds, 4410 pseudobonds, 19716 residues, 10 models
selected  
Drag select of 801 residues, 3 pseudobonds  
Drag select of 2387 residues  
Drag select of 2063 residues, 3 pseudobonds  
Drag select of 248 residues  

> select subtract #61/eEF2

27051 atoms, 3 pseudobonds, 2209 residues, 6 models selected  

> select add ssu

228416 atoms, 242995 bonds, 4410 pseudobonds, 19825 residues, 10 models
selected  
Drag select of 3023 residues, 5 pseudobonds  

> select add ssu

229015 atoms, 242995 bonds, 4410 pseudobonds, 19901 residues, 10 models
selected  

> select ssu

227531 atoms, 242995 bonds, 4410 pseudobonds, 19716 residues, 10 models
selected  

> select ~sel & ##selected

396422 atoms, 426545 bonds, 9600 pseudobonds, 32033 residues, 10 models
selected  

> select ssu

227531 atoms, 242995 bonds, 4410 pseudobonds, 19716 residues, 10 models
selected  
Drag select of 2627 residues, 5 pseudobonds  

> select add ssu

228114 atoms, 242995 bonds, 4410 pseudobonds, 19790 residues, 10 models
selected  
Drag select of 906 residues  

> select add ssu

229003 atoms, 242995 bonds, 4410 pseudobonds, 19899 residues, 10 models
selected  
Drag select of 1964 residues  

> select add ssu

228595 atoms, 242995 bonds, 4410 pseudobonds, 19852 residues, 10 models
selected  
Drag select of 3169 residues, 2 pseudobonds  

> select add ssu

228447 atoms, 242995 bonds, 4410 pseudobonds, 19827 residues, 10 models
selected  

> name frozen ssu sel

> select clear

> select add ssu

228447 atoms, 243908 bonds, 4410 pseudobonds, 19827 residues, 10 models
selected  

> hide sel cartoons

> show sel atoms

> hide sel atoms

> show sel cartoons

> hide sel atoms

> show sel atoms

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> select subtract #61/eEF2

228447 atoms, 243908 bonds, 4410 pseudobonds, 19827 residues, 10 models
selected  

> name frozen ssu sel

Drag select of 1307 residues, 2 pseudobonds  

> select add #61/eEF2

23142 atoms, 6729 bonds, 9 pseudobonds, 2156 residues, 5 models selected  

> select subb #61/eEF2

Expected an objects specifier or a keyword  

> select subtract #61/eEF2

16535 atoms, 2 pseudobonds, 1307 residues, 4 models selected  

> select add ssu

229015 atoms, 243908 bonds, 4410 pseudobonds, 19899 residues, 10 models
selected  

> select subtract #61/ASIT

227378 atoms, 242081 bonds, 4374 pseudobonds, 19822 residues, 10 models
selected  

> name frozen ssu sel

> hide sel cartoons

> show sel cartoons

> select subtract #59/PT

227378 atoms, 242081 bonds, 4374 pseudobonds, 19822 residues, 10 models
selected  

> select subtract #61/PSIT

225728 atoms, 240245 bonds, 4308 pseudobonds, 19739 residues, 10 models
selected  

> name frozen ssu sel

> color (#!58-59,61 & sel) red

> undo

> select ~sel & ##selected

398225 atoms, 428726 bonds, 9702 pseudobonds, 32010 residues, 10 models
selected  

> select subtract #61/eEF2

391618 atoms, 421997 bonds, 9693 pseudobonds, 31161 residues, 10 models
selected  

> select subtract #61/ASIT

389981 atoms, 420170 bonds, 9644 pseudobonds, 31084 residues, 10 models
selected  

> select subtract #61/PSIT

388331 atoms, 418334 bonds, 9570 pseudobonds, 31001 residues, 10 models
selected  

> select subtract #58/PT

386687 atoms, 416498 bonds, 9489 pseudobonds, 30924 residues, 10 models
selected  

> select subtract #59/PT

385043 atoms, 414662 bonds, 9412 pseudobonds, 30847 residues, 10 models
selected  

> select subtract #58/ET

383399 atoms, 412826 bonds, 9335 pseudobonds, 30770 residues, 10 models
selected  

> name frozen lsu sel

> color (#!58-59,61 & sel) red

> undo

> select ssu

225728 atoms, 240814 bonds, 4308 pseudobonds, 19739 residues, 10 models
selected  

> color (#!58-59,61 & sel) #ffffffff

> color (#!58-59,61 & sel) #ebebebff

> color (#!58-59,61 & sel) #c0c0c0ff

> color (#!58-59,61 & sel) #d6d6d6ff

> color (#!58-59,61 & sel) #c0c0c0ff

> select lsu

383399 atoms, 412826 bonds, 9335 pseudobonds, 30770 residues, 10 models
selected  

> color (#!58-59,61 & sel) #ebebebff

> select clear

> hide #!58 models

> hide #!59 models

> hide #!61 models

> show #!53 models

> show #!52 models

> show #!51 models

> show #!50 models

> color #50 silver models

> hide #!50 models

> show #!58 models

> hide #!58 models

> select #53/BT:7

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

> select up

75 atoms, 74 bonds, 15 residues, 1 model selected  

> select up

1050 atoms, 1049 bonds, 210 residues, 1 model selected  

> color #50 #ebebebff models

> show #!58 models

> show #!59 models

> show #!61 models

> hide #!58 models

> hide #!59 models

> hide #!61 models

> color sel #ffffffff

> color sel #ebebebff

> select #52/jj:134

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

> select up

103 atoms, 104 bonds, 13 residues, 1 model selected  

> select up

3383 atoms, 3453 bonds, 441 residues, 1 model selected  

> color sel #011993ff

> color sel #0096ffff

> color sel #7a81ffff

> color sel #0096ffff

> select #52/ii:5

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

> select up

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> select up

220934 atoms, 236952 bonds, 18186 residues, 1 model selected  

> select down

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> color sel orange red

> color sel red

> select #53/m:63

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

> select up

1611 atoms, 1799 bonds, 76 residues, 1 model selected  

> select up

204962 atoms, 220182 bonds, 16898 residues, 1 model selected  

> select down

1611 atoms, 1799 bonds, 76 residues, 1 model selected  

> color sel #ff7e79ff

> select #52/ii:63

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

> select up

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> color sel #ff2600ff

> select #52/jj:138

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

> select up

103 atoms, 104 bonds, 13 residues, 1 model selected  

> select up

3383 atoms, 3453 bonds, 441 residues, 1 model selected  

> color sel #76d6ffff

> color sel #0096ffff

> select #51/q3:52

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1579 atoms, 1765 bonds, 74 residues, 1 model selected  

> color sel #ff9300ff

> color sel #ffd479ff

> select #52/2:54

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

> select up

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> color sel #fffc79ff

> select #53/eI:71

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

> select up

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

> select up

1143 atoms, 1158 bonds, 154 residues, 1 model selected  

> color sel #ff85ffff

> color sel #ff8ad8ff

> color sel #ff85ffff

> color sel #d783ffff

> select #51/33:44

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1604 atoms, 1795 bonds, 75 residues, 1 model selected  

> color sel #73fa79ff

> select #52/3:30

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1593 atoms, 1779 bonds, 75 residues, 1 model selected  

> color sel #76d6ffff

> select clear

> select #52/ii:63

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

> select up

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> color sel #ff7e79ff

> color sel #ffd479ff

> color sel #ff7e79ff

> color sel #ff2600ff

> color sel #941100ff

> color sel #ff8ad8ff

> select #53/eI:72

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

> select up

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

> select up

1143 atoms, 1158 bonds, 154 residues, 1 model selected  

> color sel #d783ffff

> color sel #7a81ffff

> color sel #ff85ffff

> select #52/ii:4

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

> select up

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> color sel #ff8ad8ff

> color sel #ff2f92ff

> color sel #ff40ffff

> color sel #ff8ad8ff

> color sel #ff7e79ff

> color sel #ff9300ff

> color sel #ff2600ff

> color sel #ff9300ff

> color sel #ff2600ff

> color sel #ff2f92ff

> color sel #ff2600ff

> select #53/eI:56

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

> select up

67 atoms, 67 bonds, 9 residues, 1 model selected  

> select up

1143 atoms, 1158 bonds, 154 residues, 1 model selected  

> color sel #ff40ffff

> show #!58 models

> show #!50 models

> hide #!50 models

> show #!50 models

> hide #!50 models

> show #!50 models

> hide #!50 models

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/Manuscript1/202602_subunitcolouring.cxs
> includeMaps true

> select clear

> show #!59 models

> show #!61 models

> hide #!61 models

> hide #!59 models

> show #!59 models

> show #!61 models

> hide #!51 models

> hide #!52 models

> hide #!53 models

> show #!51 models

> hide #!51 models

> select #58/PT:48

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

> select add #61/ASIT:47

40 atoms, 42 bonds, 2 residues, 2 models selected  

> select up

3280 atoms, 3663 bonds, 153 residues, 2 models selected  

> color sel #fffc79ff

> show #!52 models

> hide #!52 models

> hide #!59 models

> show #!59 models

> hide #!59 models

> show #!59 models

> hide #!59 models

> show #!51 models

> show #!59 models

> select #59/PT:52

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

> select up

1644 atoms, 1836 bonds, 77 residues, 1 model selected  

> color sel #73fa79ff

> hide #!59 models

> select clear

> show #!52 models

> hide #!61 models

> show #!61 models

> select #58/ET:46

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #52/3:46

46 atoms, 50 bonds, 2 residues, 2 models selected  

> hide #!51 models

> hide #!52 models

> show #!52 models

> hide #!52 models

> show #!52 models

> select #52/3:46

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #58/ET:46

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #61/PSIT:46

46 atoms, 50 bonds, 2 residues, 2 models selected  

> select up

3288 atoms, 3672 bonds, 154 residues, 2 models selected  

> color sel #00fdffff

> color sel #73fdffff

> color sel #76d6ffff

> select clear

> show #!59 models

> show #!53 models

> show #!51 models

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/Manuscript1/Old_Ribofigs/202602_subunitcolouring.cxs
> includeMaps true

——— End of log from Wed Feb 4 15:33:49 2026 ———

> view name session-start

opened ChimeraX session  

> select #52/jj:377

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

> select up

111 atoms, 112 bonds, 14 residues, 1 model selected  

> select up

3383 atoms, 3453 bonds, 441 residues, 1 model selected  

> color sel #76d6ffff

> select #58/ET:45

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

> select add #52/3:44

45 atoms, 49 bonds, 2 residues, 2 models selected  

> select add #61/PSIT:46

68 atoms, 74 bonds, 3 residues, 3 models selected  

> select up

4881 atoms, 5451 bonds, 229 residues, 3 models selected  

> color sel #0096ffff

> select #53/eI:58

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

> select up

67 atoms, 67 bonds, 9 residues, 1 model selected  

> select up

1143 atoms, 1158 bonds, 154 residues, 1 model selected  

> color sel #ff85ffff

> color sel #ff8ad8ff

> color sel #d783ffff

> select #52/jj:401

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

> select up

63 atoms, 63 bonds, 9 residues, 1 model selected  

> select up

3383 atoms, 3453 bonds, 441 residues, 1 model selected  

> show sel atoms

> select up

3491 atoms, 3565 bonds, 444 residues, 1 model selected  

> show sel atoms

> color sel #76d6ffff

> hide sel atoms

> select #61/eEF2:731

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

> select up

114 atoms, 116 bonds, 14 residues, 1 model selected  

> select up

6569 atoms, 6695 bonds, 842 residues, 1 model selected  

> color sel #73fa79ff

> select #59/PT:52

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

> select #59/PT:28

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

> select add #51/33:26

40 atoms, 42 bonds, 2 residues, 2 models selected  

> color sel #00f900ff

> select up

3248 atoms, 3631 bonds, 152 residues, 2 models selected  

> color sel #009051ff

> color sel #008f00ff

> color sel #00f900ff

> color sel #008f00ff

> color sel #00f900ff

> color sel #73fa79ff

> color sel #73fcd6ff

> color sel #73fa79ff

> color sel #d4fb79ff

> color sel #73fa79ff

> select #61/eEF2:686

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

> select up

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

> select up

6569 atoms, 6695 bonds, 842 residues, 1 model selected  

> color sel #4f8f00ff

> color sel #008f00ff

> color sel #4f8f00ff

> select clear

> select #52/ii:16

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

> select up

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> color sel #ff7e79ff

> color sel #ff6666ff

> color sel #cc3300ff

> select clear

> select #52/ii:52

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

> select up

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> color sel #ff3333ff

> select clear

> select #61/eEF2:505

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

> select #52/ii:52

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

> select up

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> color sel #ff6666ff

> select clear

> select #61/eEF2:530

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

> select #52/ii:52

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

> select up

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> color sel #cc3333ff

> select clear

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/Manuscript1/Ribofigs/202602_subunitcolouring.cxs
> includeMaps true

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/60S/MultiPostProcessor_PPout_60S.mrc

Opened MultiPostProcessor_PPout_60S.mrc as #1, grid size 128,128,128, pixel 4,
shown at level 0.845, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/Decoding/MultiPostProcessor_PPout_Decoding.mrc

Opened MultiPostProcessor_PPout_Decoding.mrc as #2, grid size 128,128,128,
pixel 4, shown at level 0.896, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/Hibernating/MultiPostProcessor_PPout_Hibernating.mrc

Opened MultiPostProcessor_PPout_Hibernating.mrc as #3, grid size 128,128,128,
pixel 4, shown at level 0.916, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/Int_Post/MultiPostProcessor_PPout_Int_Post.mrc

Opened MultiPostProcessor_PPout_Int_Post.mrc as #4, grid size 128,128,128,
pixel 4, shown at level 0.889, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/Post/MultiPostProcessor_PPout_Post.mrc

Opened MultiPostProcessor_PPout_Post.mrc as #5, grid size 128,128,128, pixel
4, shown at level 0.859, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/Rotated/MultiPostProcessor_PPout_Rotated.mrc

Opened MultiPostProcessor_PPout_Rotated.mrc as #6, grid size 128,128,128,
pixel 4, shown at level 0.846, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/Translocating/MultiPostProcessor_PPout_Translocating.mrc

Opened MultiPostProcessor_PPout_Translocating.mrc as #7, grid size
128,128,128, pixel 4, shown at level 0.871, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/UnPre_cEF2/MultiPostProcessor_PPout_UnPre_cEF2.mrc

Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc as #8, grid size 128,128,128,
pixel 4, shown at level 0.91, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/UnPre_none/MultiPostProcessor_PPout_UnPre_none.mrc

Opened MultiPostProcessor_PPout_UnPre_none.mrc as #9, grid size 128,128,128,
pixel 4, shown at level 0.898, step 1, values float32  

> close #1-9

> select lsu

383399 atoms, 412826 bonds, 9335 pseudobonds, 30770 residues, 10 models
selected  

> color (#!58-59,61 & sel) #d6d6d6ff

> select ssu

225728 atoms, 240814 bonds, 4308 pseudobonds, 19739 residues, 10 models
selected  

> color (#!58-59,61 & sel) #a9a9a9ff

> select clear

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/Manuscript1/Ribofigs/202602_subunitcolouring.cxs
> includeMaps true

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/60S/MultiPostProcessor_PPout_60S.mrc

Opened MultiPostProcessor_PPout_60S.mrc as #1, grid size 128,128,128, pixel 4,
shown at level 0.845, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/Decoding/MultiPostProcessor_PPout_Decoding.mrc

Opened MultiPostProcessor_PPout_Decoding.mrc as #2, grid size 128,128,128,
pixel 4, shown at level 0.896, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/Hibernating/MultiPostProcessor_PPout_Hibernating.mrc

Opened MultiPostProcessor_PPout_Hibernating.mrc as #3, grid size 128,128,128,
pixel 4, shown at level 0.916, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/Int_Post/MultiPostProcessor_PPout_Int_Post.mrc

Opened MultiPostProcessor_PPout_Int_Post.mrc as #4, grid size 128,128,128,
pixel 4, shown at level 0.889, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/Post/MultiPostProcessor_PPout_Post.mrc

Opened MultiPostProcessor_PPout_Post.mrc as #5, grid size 128,128,128, pixel
4, shown at level 0.859, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/Rotated/MultiPostProcessor_PPout_Rotated.mrc

Opened MultiPostProcessor_PPout_Rotated.mrc as #6, grid size 128,128,128,
pixel 4, shown at level 0.846, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/Translocating/MultiPostProcessor_PPout_Translocating.mrc

Opened MultiPostProcessor_PPout_Translocating.mrc as #7, grid size
128,128,128, pixel 4, shown at level 0.871, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/UnPre_cEF2/MultiPostProcessor_PPout_UnPre_cEF2.mrc

Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc as #8, grid size 128,128,128,
pixel 4, shown at level 0.91, step 1, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/MultiPostProcessor/20260204_SpeciesForM/UnPre_none/MultiPostProcessor_PPout_UnPre_none.mrc

Opened MultiPostProcessor_PPout_UnPre_none.mrc as #9, grid size 128,128,128,
pixel 4, shown at level 0.898, step 1, values float32  

> volume level 0.6

> fitmap #1-49 inMap #50 eachModel true

Fit map MultiPostProcessor_PPout_60S.mrc in map Stable_60S.mrc using 45019
points  
correlation = 0.9792, correlation about mean = 0.6732, overlap = 3.084e+04  
steps = 60, shift = 11.2, angle = 0.347 degrees  
  
Position of MultiPostProcessor_PPout_60S.mrc (#1) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99998258 0.00350909 0.00474719 -9.58200270  
-0.00350249 0.99999289 -0.00139727 6.38704110  
-0.00475206 0.00138062 0.99998776 -5.53422025  
Axis 0.22902732 0.78317944 -0.57807997  
Axis point -439.81020091 0.00000000 2306.64258437  
Rotation angle (degrees) 0.34747506  
Shift along axis 6.00688077  
  
Fit map MultiPostProcessor_PPout_Decoding.mrc in map Stable_60S.mrc using
58200 points  
correlation = 0.7973, correlation about mean = 0.3491, overlap = 2.848e+04  
steps = 64, shift = 1.73, angle = 1.23 degrees  
  
Position of MultiPostProcessor_PPout_Decoding.mrc (#2) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99978338 0.01754097 0.01120287 -7.63491730  
-0.01760124 0.99983102 0.00530345 4.59034830  
-0.01110795 -0.00549948 0.99992318 3.59329984  
Axis -0.25120034 0.51879292 -0.81716112  
Axis point 216.60492651 418.41715509 0.00000000  
Rotation angle (degrees) 1.23210437  
Shift along axis 1.36302911  
  
Fit map MultiPostProcessor_PPout_Hibernating.mrc in map Stable_60S.mrc using
61332 points  
correlation = 0.8013, correlation about mean = 0.3742, overlap = 2.998e+04  
steps = 116, shift = 2.08, angle = 0.355 degrees  
  
Position of MultiPostProcessor_PPout_Hibernating.mrc (#3) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99998540 0.00390522 0.00373423 -2.77891118  
-0.00391658 0.99998771 0.00304124 2.06401939  
-0.00372231 -0.00305582 0.99998840 1.37709525  
Axis -0.49138688 0.60095388 -0.63039143  
Axis point 258.80057658 493.89313962 0.00000000  
Rotation angle (degrees) 0.35546108  
Shift along axis 1.73779192  
  
Fit map MultiPostProcessor_PPout_Int_Post.mrc in map Stable_60S.mrc using
58966 points  
correlation = 0.8005, correlation about mean = 0.3796, overlap = 2.858e+04  
steps = 96, shift = 1.92, angle = 0.711 degrees  
  
Position of MultiPostProcessor_PPout_Int_Post.mrc (#4) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99992955 0.01058124 0.00537799 -4.70979073  
-0.01060077 0.99993727 0.00361524 3.44441183  
-0.00533940 -0.00367200 0.99997900 2.04384340  
Axis -0.29345807 0.43159025 -0.85300189  
Axis point 276.64661390 415.74052028 0.00000000  
Rotation angle (degrees) 0.71141168  
Shift along axis 1.12529839  
  
Fit map MultiPostProcessor_PPout_Post.mrc in map Stable_60S.mrc using 58643
points  
correlation = 0.8006, correlation about mean = 0.3306, overlap = 2.743e+04  
steps = 76, shift = 1.92, angle = 1.04 degrees  
  
Position of MultiPostProcessor_PPout_Post.mrc (#5) relative to Stable_60S.mrc
(#50) coordinates:  
Matrix rotation and translation  
0.99985047 0.01308904 0.01130090 -6.69830250  
-0.01314845 0.99990004 0.00519936 3.58665015  
-0.01123172 -0.00534717 0.99992263 3.38993247  
Axis -0.29168425 0.62318224 -0.72564743  
Axis point 187.21836504 475.35711722 0.00000000  
Rotation angle (degrees) 1.03588809  
Shift along axis 1.72903021  
  
Fit map MultiPostProcessor_PPout_Rotated.mrc in map Stable_60S.mrc using 56551
points  
correlation = 0.8023, correlation about mean = 0.3251, overlap = 2.654e+04  
steps = 84, shift = 2.19, angle = 0.302 degrees  
  
Position of MultiPostProcessor_PPout_Rotated.mrc (#6) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99999884 0.00074899 -0.00132618 -1.12946951  
-0.00075568 0.99998698 -0.00504576 3.16815051  
0.00132238 0.00504675 0.99998639 -1.95276683  
Axis 0.95734523 -0.25123442 -0.14272831  
Axis point 0.00000000 433.61915370 547.17316851  
Rotation angle (degrees) 0.30201266  
Shift along axis -1.59852561  
  
Fit map MultiPostProcessor_PPout_Translocating.mrc in map Stable_60S.mrc using
55898 points  
correlation = 0.7969, correlation about mean = 0.3519, overlap = 2.701e+04  
steps = 80, shift = 1.98, angle = 0.548 degrees  
  
Position of MultiPostProcessor_PPout_Translocating.mrc (#7) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99997953 0.00284971 -0.00572847 -0.55014406  
-0.00289036 0.99997062 -0.00710002 3.98692410  
0.00570806 0.00711643 0.99995839 -3.14064689  
Axis 0.74325810 -0.59791934 -0.30009974  
Axis point 0.00000000 521.70794826 403.56130181  
Rotation angle (degrees) 0.54796266  
Shift along axis -1.85025072  
  
Fit map MultiPostProcessor_PPout_UnPre_cEF2.mrc in map Stable_60S.mrc using
58314 points  
correlation = 0.7884, correlation about mean = 0.3212, overlap = 2.842e+04  
steps = 64, shift = 2.57, angle = 0.969 degrees  
  
Position of MultiPostProcessor_PPout_UnPre_cEF2.mrc (#8) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99992462 0.00202807 0.01210961 -4.04107372  
-0.00216874 0.99993019 0.01161481 0.12051900  
-0.01208521 -0.01164020 0.99985922 5.39644993  
Axis -0.68760953 0.71539799 -0.12409213  
Axis point 466.60515624 -0.00000000 211.96194507  
Rotation angle (degrees) 0.96892031  
Shift along axis 2.19524288  
  
Fit map MultiPostProcessor_PPout_UnPre_none.mrc in map Stable_60S.mrc using
58116 points  
correlation = 0.7946, correlation about mean = 0.3249, overlap = 2.832e+04  
steps = 96, shift = 2.21, angle = 0.87 degrees  
  
Position of MultiPostProcessor_PPout_UnPre_none.mrc (#9) relative to
Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.99991844 0.00671877 0.01086139 -4.97075525  
-0.00680768 0.99994346 0.00816940 1.70192430  
-0.01080589 -0.00824267 0.99990764 4.18998849  
Axis -0.54056373 0.71365443 -0.44552016  
Axis point 468.57087156 0.00000000 359.89805086  
Rotation angle (degrees) 0.86981277  
Shift along axis 2.03487150  
  

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!6 models

> hide #!5 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!51 models

> hide #!52 models

> hide #!53 models

> hide #!58 models

> hide #!59 models

> hide #!61 models

> lighting full

[Repeated 1 time(s)]

> lighting soft

> lighting simple

> lighting soft

> graphics silhouettes false

> lighting full

> lighting simple

> color #1 #d6d6d6ff models

> color #1 silver models

> lighting full

> lighting soft

> lighting simple

> hide #!1 models

> show #!2 models

> lighting soft

> show #!1 models

> hide #!2 models

> lighting soft

> graphics silhouettes true

> hide #!1 models

> show #!2 models

> ui tool show "Color Zone"

> show #!58 models

> hide #!2 models

> select #58 7 ssu

Expected a keyword  

> select #58 & ssu

76502 atoms, 81635 bonds, 1405 pseudobonds, 6670 residues, 3 models selected  

> select add #58 & lsu

205848 atoms, 221047 bonds, 4355 pseudobonds, 16928 residues, 3 models
selected  

> hide #!58 models

> show #!51 models

> hide #!51 models

> show #!52 models

Drag select of 668 residues  

> show #!58 models

> hide #!58 models

> select subtract #52/3

212463 atoms, 221047 bonds, 4355 pseudobonds, 17521 residues, 4 models
selected  

> show #!2 models

> color zone #2 near sel distance 24

> color zone #2 near sel distance 5

> color zone #2 near sel distance 50

[Repeated 1 time(s)]

> volume splitbyzone #2

Opened MultiPostProcessor_PPout_Decoding.mrc 0 as #10.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 1 as #10.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 2 as #10.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 3 as #10.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 4 as #10.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 5 as #10.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!10.1 models

> color #10.2 #d6d6d618 models

> color #10.2 #d6d6d619 models

> color #10.2 #d6d6d632 models

> lighting full

> hide #!52 models

> color #10.3 #a9a9a937 models

> color #10.3 #a9a9a95a models

> color #10.5 #ff3333ff models

> color #10.5 #ff6666ff models

> color #10.5 #cc3333ff models

> color #10.5 #660000ff models

> color #10.5 #cc6666ff models

> color #10.5 #ff6666ff models

> color #10.5 #cc6666ff models

> color #10.5 #ff9999ff models

> color #10.5 #ff7e79ff models

> color #10.5 #ffccccff models

> color #10.5 #ff9999ff models

> color #10.5 #cc6666ff models

> color #10.5 #ff7e79ff models

> color #10.5 #ff6666ff models

> color #10.5 #cc6666ff models

> color #10.6 #993366ff models

> color #10.6 #ff85ffff models

> show #!53 models

> hide #!53 models

> hide #!10 models

> show #!3 models

> show #!61 models

> hide #!3 models

> select #61 & ssu

72156 atoms, 76975 bonds, 1501 pseudobonds, 6327 residues, 4 models selected  

> select add #61 & lsu

197172 atoms, 211322 bonds, 4937 pseudobonds, 16594 residues, 4 models
selected  

> select add #61/eEF2

203779 atoms, 218051 bonds, 4944 pseudobonds, 17443 residues, 4 models
selected  

> show #!53 models

> hide #!61 models

> select add #53/eI

204922 atoms, 219209 bonds, 4944 pseudobonds, 17597 residues, 5 models
selected  

> show #!3 models

> hide #!3 models

> show #!61 models

> show #!3 models

> show #!2 models

> hide #!2 models

> select add #53/BT

205972 atoms, 220258 bonds, 4944 pseudobonds, 17807 residues, 5 models
selected  

> color zone #3 near sel distance 50

> hide #!53 models

> hide #!61 models

> volume splitbyzone #3

Opened MultiPostProcessor_PPout_Hibernating.mrc 0 as #11.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 1 as #11.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 2 as #11.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 3 as #11.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 4 as #11.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 5 as #11.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 6 as #11.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!11.1 models

> hide #!11.7 models

> show #!11.7 models

> hide #!11.7 models

> show #!11.7 models

> hide #!11.7 models

> show #!11.7 models

> hide #!11.7 models

> show #!11.7 models

> hide #!11.7 models

> show #!11.7 models

> show #!2 models

> hide #!11 models

> hide #!2 models

> show #!10 models

> close #10-11

> show #!52 models

> show #!2 models

> hide #!2 models

> select #52/ii:22

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

> select up

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> color sel #945200ff

> color sel #941100ff

> undo

[Repeated 9 time(s)]

> select add #53

408741 atoms, 438233 bonds, 10174 pseudobonds, 34341 residues, 8 models
selected  

> select subtract #53

203779 atoms, 218051 bonds, 4944 pseudobonds, 17443 residues, 4 models
selected  

> select add #61

207066 atoms, 221714 bonds, 5069 pseudobonds, 17603 residues, 4 models
selected  

> select subtract #61

Nothing selected  

> hide #!2 models

> show #!51 models

> show #!52 models

> show #!53 models

> show #!59 models

> show #!61 models

> show #!58 models

> hide #!58 models

> hide #!59 models

> hide #!61 models

> select #52/ii:56

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

> select up

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> select up

220934 atoms, 236952 bonds, 18186 residues, 1 model selected  

> select down

1616 atoms, 1806 bonds, 76 residues, 1 model selected  

> color sel #000000ff

> color sel #941100ff

> select #52/jj:124

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

> select up

50 atoms, 50 bonds, 7 residues, 1 model selected  

> select up

3383 atoms, 3453 bonds, 441 residues, 1 model selected  

> select up

3491 atoms, 3565 bonds, 444 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> color sel #942193ff

> color sel #ff40ffff

> color sel #ff85ffff

> color sel #d783ffff

> color sel #7a81ffff

> color sel #d783ffff

> select #53/eI:75

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

> select up

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

> select up

1143 atoms, 1158 bonds, 154 residues, 1 model selected  

> color sel #9437ffff

> color sel #7a81ffff

> color sel #ff85ffff

> color sel #ff8ad8ff

> color sel #ff2f92ff

> color sel #941751ff

> color sel #011993ff

> color sel #76d6ffff

> hide #!51 models

> show #!51 models

> hide #!51 models

> hide #!52 models

> hide #!53 models

> show #!58 models

> hide #!58 models

> show #!59 models

> hide #!59 models

> show #!61 models

> show #!58 models

> show #!59 models

> hide #!58 models

> hide #!59 models

> hide #!61 models

> show #!2 models

> hide #!2 models

> show #!58 models

> select #58 & ssu

76502 atoms, 81635 bonds, 1405 pseudobonds, 6670 residues, 3 models selected  

> select add #58 & lsu

205848 atoms, 221047 bonds, 4355 pseudobonds, 16928 residues, 3 models
selected  

> hide #!58 models

> show #!52 models

> hide #!52 models

> show #!58 models

> show #!53 models

> hide #!58 models

> show #!59 models

> hide #!59 models

> select #53/BT:14

5 atoms, 4 bonds, 1 residue, 1 model selected  
Drag select of 276 residues  

> select subtract $53/eI

Expected an objects specifier or a keyword  

> select subtract #53/eI

1050 atoms, 210 residues, 1 model selected  

> color sel #d6d6d6ff

> color sel #a9a9a9ff

> color sel #d6d6d6ff

> select clear

> hide #!53 models

> show #!58 models

> show #!52 models

> select #58 & ssu

76502 atoms, 81635 bonds, 1405 pseudobonds, 6670 residues, 3 models selected  

> select add #58 & lsu

205848 atoms, 221047 bonds, 4355 pseudobonds, 16928 residues, 3 models
selected  

> hide #!58 models

Drag select of 668 residues  

> select subtract #52/3

212463 atoms, 221047 bonds, 4355 pseudobonds, 17521 residues, 4 models
selected  

> show #!53 models

> select #53/BT:10

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

> select up

75 atoms, 74 bonds, 15 residues, 1 model selected  

> select up

1050 atoms, 1049 bonds, 210 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> undo

[Repeated 5 time(s)]

> show #!58 models

> hide #!58 models

> select add #53BT

Expected an objects specifier or a keyword  

> select add #53/BT

213513 atoms, 222096 bonds, 4355 pseudobonds, 17731 residues, 5 models
selected  

> show #!2 models

> color zone #2 near sel distance 50

> hide #!52 models

> hide #!53 models

> volume splitbyzone #2

Opened MultiPostProcessor_PPout_Decoding.mrc 0 as #10.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 1 as #10.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 2 as #10.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 3 as #10.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 4 as #10.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Decoding.mrc 5 as #10.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!10.1 models

> hide #!10.6 models

> show #!10.6 models

> color #10.2 #d6d6d632 models

> lighting full

> color #10.2 #d6d6d633 models

> color #10.3 #a9a9a959 models

> hide #!10 models

> show #!3 models

> show #!61 models

> select #61 & ssu

72156 atoms, 76975 bonds, 1501 pseudobonds, 6327 residues, 4 models selected  

> select add #61 & lsu

197172 atoms, 211322 bonds, 4937 pseudobonds, 16594 residues, 4 models
selected  

> hide #!3 models

> select add #61/eEF2

203779 atoms, 218051 bonds, 4944 pseudobonds, 17443 residues, 4 models
selected  

> show #!53 models

> hide #!61 models

Drag select of 364 residues  

> hide #!53 models

> show #!3 models

> color zone #3 near sel distance 50

> volume splitbyzone #3

Opened MultiPostProcessor_PPout_Hibernating.mrc 0 as #11.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 1 as #11.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 2 as #11.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 3 as #11.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Hibernating.mrc 4 as #11.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!11.1 models

> color #11.2 #d6d6d630 models

> color #11.2 #d6d6d634 models

> color #11.2 #d6d6d633 models

> color #11.3 #a9a9a956 models

> color #11.3 #a9a9a959 models

> hide #!11 models

> show #!4 models

> show #!61 models

> hide #!4 models

> show #!4 models

> hide #!61 models

> select clear

> show #!58 models

> hide #!58 models

> show #!59 models

> show #!61 models

> hide #!59 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> select #61 & ssu

72156 atoms, 76975 bonds, 1501 pseudobonds, 6327 residues, 4 models selected  

> select add #61/eEF2

78763 atoms, 83704 bonds, 1508 pseudobonds, 7176 residues, 4 models selected  

> select add #61 & lsu

203779 atoms, 218051 bonds, 4944 pseudobonds, 17443 residues, 4 models
selected  

> show #!52 models

> hide #!61 models

> hide #!4 models

Drag select of 151 residues  

> show #!61 models

> hide #!61 models

> show #!61 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!53 models

> hide #!61 models

> hide #!52 models

> hide #!53 models

> show #!52 models

> show #!4 models

> color zone #4 near sel distance 50

> hide #!52 models

> show #!53 models

> hide #!4 models

> show #!52 models

Drag select of 43 residues  

> select subtract #53/eI:4

207198 atoms, 218051 bonds, 4944 pseudobonds, 17636 residues, 6 models
selected  

> show #!4 models

> color zone #4 near sel distance 50

> hide #!4 models

Drag select of 43 residues  

> select add #53/BT:20

207408 atoms, 218055 bonds, 4944 pseudobonds, 17678 residues, 6 models
selected  

> show #!4 models

> color zone #4 near sel distance 50

> volume splitbyzone #4

Opened MultiPostProcessor_PPout_Int_Post.mrc 0 as #12.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 1 as #12.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 2 as #12.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 3 as #12.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 4 as #12.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 5 as #12.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Int_Post.mrc 6 as #12.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!12.1 models

> color #12.2 #d6d6d633 models

> color #12.3 #a9a9a959 models

> hide #!52 models

> hide #!53 models

> hide #!12 models

> show #!5 models

> show #!4 models

> hide #!4 models

> hide #!5 models

> show #!59 models

> show #!58 models

> hide #!59 models

> show #!5 models

> select #58 & lsu

129346 atoms, 139412 bonds, 2950 pseudobonds, 10258 residues, 3 models
selected  

> select add #58 & ssu

205848 atoms, 221047 bonds, 4355 pseudobonds, 16928 residues, 3 models
selected  

> hide #!58 models

> show #!53 models

> select add #53/BT

206898 atoms, 222096 bonds, 4355 pseudobonds, 17138 residues, 4 models
selected  

> hide #!53 models

> show #!52 models

> select add #52/2

208514 atoms, 223902 bonds, 4422 pseudobonds, 17214 residues, 6 models
selected  

> hide #!52 models

> show #!4 models

> hide #!4 models

> color zone #5 near sel distance 50

> hide #!12.7 models

> show #!12.7 models

> hide #!12.7 models

> show #!12.7 models

> hide #!12 models

> volume splitbyzone #5

Opened MultiPostProcessor_PPout_Post.mrc 0 as #13.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 1 as #13.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 2 as #13.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Post.mrc 3 as #13.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  

> hide #!13.1 models

> color #13.2 #d6d6d632 models

> color #13.2 #d6d6d633 models

> color #13.3 #a9a9a94a models

> color #13.3 #a9a9a95a models

> color #13.3 #a9a9a959 models

> hide #!13 models

> show #!6 models

> show #!59 models

> select #59 & lsu

129037 atoms, 139067 bonds, 2949 pseudobonds, 10245 residues, 3 models
selected  

> select add #59 & ssu

206107 atoms, 221271 bonds, 4351 pseudobonds, 16987 residues, 3 models
selected  

> hide #!59 models

> hide #!6 models

> show #!51 models

> show #!6 models

> hide #!6 models

> show #!59 models

> hide #!59 models

Drag select of 149 residues  

> show #!59 models

> show #!6 models

> color zone #6 near sel distance 50

> volume splitbyzone #6

Opened MultiPostProcessor_PPout_Rotated.mrc 0 as #14.1, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 1 as #14.2, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 2 as #14.3, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 3 as #14.4, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Rotated.mrc 4 as #14.5, grid size 128,128,128,
pixel 4, shown at level 0.6, step 1, values float32  

> hide #!14.1 models

> color #14.2 #d6d6d639 models

> color #14.2 #d6d6d634 models

> color #14.2 #d6d6d633 models

> color #14.3 #a9a9a95a models

> hide #!51 models

> color #14.3 #a9a9a959 models

> hide #!59 models

> show #!51 models

> hide #!14 models

> show #!7 models

> show #!59 models

> hide #!59 models

> show #!59 models

> show #!61 models

> select add #61/eEF2

215897 atoms, 228000 bonds, 4358 pseudobonds, 17985 residues, 6 models
selected  

> color zone #7 near sel distance 50

> hide #!59 models

> hide #!51 models

> hide #!61 models

> volume splitbyzone #7

Opened MultiPostProcessor_PPout_Translocating.mrc 0 as #15.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 1 as #15.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 2 as #15.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 3 as #15.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 4 as #15.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 5 as #15.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 6 as #15.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> close #15

> show #!7 models

> show #!61 models

> hide #!7 models

> show #!51 models

> hide #!51 models

> show #!59 models

> hide #!59 models

> hide #!61 models

> show #!61 models

> show #!51 models

> name frozen temprot sel

Drag select of 580 residues, 1 pseudobonds  

> select sel & #61/eEF2

526 atoms, 532 bonds, 64 residues, 1 model selected  

> select sel | #61/eEF2

13555 atoms, 14192 bonds, 112 pseudobonds, 1365 residues, 6 models selected  

> select sel & #61/eEF2

6607 atoms, 6729 bonds, 7 pseudobonds, 849 residues, 2 models selected  
Drag select of 531 residues, 1 pseudobonds  

> select sel & #61/eEF2

681 atoms, 691 bonds, 84 residues, 1 model selected  

> select #61/eEF2 | sel

6607 atoms, 6729 bonds, 7 pseudobonds, 849 residues, 2 models selected  

> undo

> name frozen ef2excess sel

> select temprot

215897 atoms, 231560 bonds, 4468 pseudobonds, 17985 residues, 7 models
selected  

> select subtract ef2excess

215216 atoms, 230860 bonds, 4468 pseudobonds, 17901 residues, 7 models
selected  

> show #!7 models

> color zone #7 near sel distance 50

> volume splitbyzone #7

Opened MultiPostProcessor_PPout_Translocating.mrc 0 as #15.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 1 as #15.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 2 as #15.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 3 as #15.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 4 as #15.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 5 as #15.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_Translocating.mrc 6 as #15.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!15.1 models

> hide #!51 models

> hide #!61 models

> color #15.2 #d6d6d633 models

> color #15.3 #a9a9a959 models

> hide #!15.5 models

> show #!15.5 models

> hide #!15.5 models

> show #!15.5 models

> show #!51 models

> hide #!51 models

> show #!59 models

> hide #!59 models

> show #!61 models

> hide #!61 models

> hide #!15.5 models

> hide #!15 models

> show #!8 models

> show #!58 models

> select #58 & lsu

129346 atoms, 139412 bonds, 2950 pseudobonds, 10258 residues, 3 models
selected  

> select add #58 & ssu

205848 atoms, 221047 bonds, 4355 pseudobonds, 16928 residues, 3 models
selected  

> hide #!58 models

> hide #!8 models

> show #!53 models

> show #!52 models

> hide #!52 models

> show #!51 models

> hide #!51 models

> show #!52 models

> show #!8 models

> hide #!8 models

> hide #!53 models

> show #!53 models

> hide #!52 models

Drag select of 364 residues  

> show #!52 models

> hide #!53 models

> select add #52/2

209657 atoms, 222853 bonds, 4422 pseudobonds, 17368 residues, 6 models
selected  

> hide #!52 models

> show #!59 models

> hide #!59 models

> show #!51 models

> hide #!51 models

> show #!61 models

> show #!53 models

> hide #!53 models

> name frozen unrno2 sel

Drag select of 2302 residues, 9 pseudobonds  

> show #!8 models

> hide #!61 models

> show #!52 models

> select ef2excess

681 atoms, 691 bonds, 84 residues, 1 model selected  

> select unrno2

209657 atoms, 225060 bonds, 4422 pseudobonds, 17368 residues, 6 models
selected  

> hide #!8 models

> select add #52/jj

213148 atoms, 228625 bonds, 4426 pseudobonds, 17812 residues, 7 models
selected  

> show #!8 models

> color zone #8 near sel distance 50

> hide #!52 models

> show #!53 models

> hide #!8 models

Drag select of 76 residues  

> show #!7 models

> color zone #8 near sel distance 50

> hide #!7 models

> show #!8 models

> volume splitbyzone #8

Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 0 as #16.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 1 as #16.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 2 as #16.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 3 as #16.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 4 as #16.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 5 as #16.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_cEF2.mrc 6 as #16.7, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!16.1 models

> color #16.2 #d6d6d633 models

> color #16.3 #a9a9a958 models

> hide #!53 models

> color #16.3 #a9a9a957 models

> color #16.5 #4f8f00ff models

> show #!15 models

> color #16.5 #8efa00ff models

> color #16.5 #009193ff models

> color #16.5 #008f00ff models

> color #16.5 #4f8f00ff models

[Repeated 1 time(s)]

> color #15.4 #008f00ff models

> color #15.4 #4f8f00ff models

> undo

[Repeated 6 time(s)]

> color #15.4 #008f00ff models

> color #15.4 #4f8f00ff models

> hide #!15 models

> color #16.5 #0096ffff models

> color #16.5 #4f8f00ff models

> show #!10 models

> hide #!10 models

> show #!15 models

> hide #!15 models

> show #!12 models

> hide #!12 models

> color #16.7 #009193ff models

> show #!12 models

> hide #!12 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> hide #!16 models

> show #!52 models

> hide #!52 models

> select clear

> show #!53 models

> select #53/eI:19

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

> select up

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

> select up

1143 atoms, 1158 bonds, 154 residues, 1 model selected  

> color #16.7 #009193ff models

> color #16.7 #011993ff models

> color #16.7 #009193ff models

> show #!15 models

> show #!16 models

> color #16.7 #ff40ffff models

> color #16.7 #009193ff models

> hide #!15 models

> hide #!16 models

> ui tool show "Color Actions"

> color sel #009051ff

> color sel #009193ff

> show #!59 models

> show #!61 models

> hide #!59 models

> select #61/eEF2:351

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

> select up

68 atoms, 69 bonds, 9 residues, 1 model selected  

> select up

6569 atoms, 6695 bonds, 842 residues, 1 model selected  

> color sel #00fdffff

> color sel #4f8f00ff

> select clear

> hide #!53 models

> hide #!61 models

> show #!9 models

> select temprot

215897 atoms, 231560 bonds, 4468 pseudobonds, 17985 residues, 7 models
selected  

> show #!61 models

> show #!59 models

> select subtract #61/eEF2

209290 atoms, 224831 bonds, 4461 pseudobonds, 17136 residues, 5 models
selected  

> select unrno2

209657 atoms, 225060 bonds, 4422 pseudobonds, 17368 residues, 6 models
selected  

> show #!53 models

> hide #!59 models

> hide #!61 models

> hide #!9 models

Drag select of 76 residues  

> color zone #9 near sel distance 50

> show #!9 models

> hide #!53 models

> volume splitbyzone #9

Opened MultiPostProcessor_PPout_UnPre_none.mrc 0 as #17.1, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 1 as #17.2, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 2 as #17.3, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 3 as #17.4, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 4 as #17.5, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  
Opened MultiPostProcessor_PPout_UnPre_none.mrc 5 as #17.6, grid size
128,128,128, pixel 4, shown at level 0.6, step 1, values float32  

> hide #!17.1 models

> color #17.2 #d6d6d634 models

> color #17.2 #d6d6d633 models

> color #17.3 #a9a9a95a models

> color #17.3 #a9a9a959 models

> hide #!17 models

> show #!16 models

> hide #!16 models

> show #!15 models

> hide #!15 models

> show #!14 models

> hide #!14 models

> show #!15 models

> hide #!15 models

> show #!14 models

> hide #!14 models

> show #!13 models

> hide #!13 models

> show #!11 models

> color #11.5 #009193ff models

> hide #!11 models

> show #!10 models

> show #!11 models

> show #!12 models

> show #!13 models

> show #!14 models

> show #!15 models

> show #!16 models

> show #!17 models

> show #!1 models

> hide #!1 models

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/Manuscript1/Ribofigs/PlaceholderDensitiesColoured.cxs
> includeMaps true

——— End of log from Wed Feb 4 17:42:03 2026 ———

> view name session-start

opened ChimeraX session  

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes true depthJump 0.01

> graphics silhouettes true depthJump 0.005

> hide #!11 models

> hide #!12 models

> hide #!14 models

> hide #!13 models

> hide #!16 models

> hide #!17 models

> hide #!15 models

> graphics silhouettes true depthJump 0.01

> show #!11 models

> show #!12 models

> show #!13 models

> hide #!13 models

> show #!13 models

> show #!14 models

> show #!15 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!15 models

> hide #!14 models

> hide #!12 models

> hide #!11 models

> hide #!10 models

> show #!12 models

> hide #!16 models

> show #!14 models

> show #!15 models

> hide #!13 models

> hide #!12 models

> color #14.4 #ff9300ff models

[Repeated 1 time(s)]

> color #15.6 #ff9300ff models

> lighting soft

> lighting flat

> lighting full

> lighting flat

> lighting soft

> lighting full

> lighting soft

> lighting simple

> lighting full

> color #15.4 #929000ff models

> color #15.4 #4f8f00ff models

> color #15.4 #009051ff models

> color #15.4 #00fa92ff models

> undo

[Repeated 7 time(s)]

> show #!7 models

> hide #!7 models

> hide #!15 models

> color #14.4 #ff9300ff models

> color #15.6 #ff9300ff models

> show #!15 models

> hide #!14 models

> show #!12 models

> color #15.4 #008f00ff models

> color #15.4 #4f8f00ff models

> color #15.4 #929000ff models

> color #15.4 #4f8f00ff models

> lighting full

> color #15.4 #008f00ff models

> color #15.4 #929000ff models

> color #15.4 #fffb00ff models

> color #15.4 #4f8f00ff models

> color #15.4 #336600ff models

> color #15.4 #4f8f00ff models

[Repeated 1 time(s)]

> hide #!15 models

> hide #!12 models

> show #!11 models

> color #15.4 #008f00ff models

> color #15.4 #4f8f00ff models

> show #!15 models

> hide #!15 models

> hide #!11 models

> show #!11 models

> color #11.4 #929000ff models

> color #11.4 #4f8f00ff models

> color #11.4 #336600ff models

> color #11.4 #669933ff models

> color #11.4 #99cc33ff models

> color #11.4 #ccff99ff models

> color #11.4 #669900ff models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> color #15.4 #669900ff models

> show #!12 models

> color #12.4 #669900ff models

> hide #!12 models

> show #!15 models

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting full

> color #15.6 #ff9900ff models

> color #15.6 #cc9933ff models

> color #15.6 #ff9933ff models

> color #14.4 #ff9933ff models

> show #!14 models

> hide #!15 models

> hide #!11 models

> color #15.7 #66ff66ff models

> color #15.7 #00cc00ff models

> color #15.7 #66ff66ff models

> color #14.5 #33ff33ff models

> color #14.5 #00cc00ff models

> color #14.5 #66ff66ff models

> color #14.5 #33cc33ff models

> color #14.5 #99ff99ff models

[Repeated 1 time(s)]

> color #14.5 #66cc66ff models

> color #14.5 #336633ff models

> color #14.5 #33cc33ff models

> color #14.5 #339900ff models

> color #14.5 #66ff33ff models

> color #14.5 #ccffccff models

> color #14.5 #99cc99ff models

> color #14.5 #73fa79ff models

> color #14.5 #00fa92ff models

> color #14.5 #d4fb79ff models

> color #14.5 #73fa79ff models

[Repeated 1 time(s)]

> color #14.5 #66ff66ff models

> color #14.5 #66ff99ff models

> color #14.5 #00cc33ff models

> color #14.5 #009933ff models

> color #14.5 #00cc33ff models

> color #14.5 #33cc33ff models

> color #14.5 #99ff99ff models

> color #14.5 #66cc66ff models

> show #!12 models

> hide #!12 models

> color #14.5 #99ff99ff models

> graphics silhouettes true depthJump 0.005

> color #14.5 #73fcd6ff models

> color #14.5 #73fa79ff models

> color #14.5 #66ff66ff models

> color #14.5 #73fa79ff models

> color #14.5 #33ff33ff models

> color #14.5 #66ff66ff models

> color #14.5 #66ff99ff models

> color #14.5 #33ff66ff models

> color #14.5 #66ff99ff models

> color #14.5 #33cc66ff models

> color #14.5 #33ff99ff models

> color #14.5 #99ffccff models

> color #14.5 #99ff99ff models

> color #14.5 #66cc66ff models

> color #14.5 #99ff99ff models

> color #14.5 #33cc33ff models

> color #14.5 #99ff99ff models

> lighting full

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting simple

> color #14.5 #73fa79ff models

> lighting full

[Repeated 2 time(s)]

> lighting soft

> lighting simple

> lighting full

> color #14.5 #66ff66ff models

> color #14.5 #99ff99ff models

> color #14.5 #66ff66ff models

> color #14.5 #73fa79ff models

> color #15.7 #73fa79ff models

> hide #!14 models

> show #!15 models

> show #!12 models

> show #!13 models

> hide #!13 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!10 models

> hide #!10 models

> show #!10 models

> show #!16 models

> color #16.5 #669900ff models

> show #!17 models

> hide #!17 models

> hide #!16 models

> show #!16 models

> show #!11 models

> show #!17 models

> show #!13 models

> show #!14 models

> hide #!11 models

> hide #!12 models

> hide #!15 models

> hide #!13 models

> hide #!14 models

> hide #!16 models

> hide #!17 models

> graphics silhouettes true depthJump 0.005

> lighting full

> graphics silhouettes true depthJump 0.008

> graphics silhouettes true depthJump 0.01

> lighting full

> graphics silhouettes true depthJump 0.01

> color #10.5 #990000ff models

> color #10.5 #941100ff models

[Repeated 1 time(s)]

> show #!11 models

> show #!12 models

> show #!13 models

> show #!14 models

> show #!15 models

> show #!16 models

> show #!17 models

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> hide #!17 models

> surface dust #15.2 size 40

> surface dust #15.3 size 40

> surface dust #15.4 size 40

> surface dust #15.6 size 40

> surface dust #15.7 size 40

> show #!16 models

> show #!17 models

> hide #!17 models

> hide #!16 models

> show #!14 models

> show #!13 models

> show #!12 models

> show #!11 models

> show #!10 models

> show #!16 models

> show #!17 models

> surface dust #10.2 size 40

> surface dust #10.3 size 40

> surface dust #10.4 size 40

> surface dust #10.5 size 40

> surface dust #10.6 size 40

> surface dust #11.2 size 40

> surface dust #11.3 size 40

> surface dust #11.4 size 40

> surface dust #11.5 size 40

> surface dust #12.2 size 40

> surface dust #12.3 size 40

> surface dust #12.4 size 40

> surface dust #12.5 size 40

> surface dust #12.6 size 40

> surface dust #12.7 size 40

> surface dust #13.2 size 40

> surface dust #13.3 size 40

> surface dust #13.4 size 40

> surface dust #14.2 size 40

> surface dust #14.3 size 40

> surface dust #14.4 size 40

> surface dust #14.5 size 40

> surface dust #15.2 size 40

> surface dust #15.3 size 40

> surface dust #15.4 size 40

> surface dust #15.6 size 40

> surface dust #15.7 size 40

> surface dust #16.2 size 40

> surface dust #16.3 size 40

> surface dust #16.4 size 40

> surface dust #16.5 size 40

> surface dust #16.6 size 40

> surface dust #16.7 size 40

> surface dust #17.2 size 40

> surface dust #17.3 size 40

> surface dust #17.4 size 40

> surface dust #17.5 size 40

> surface dust #17.6 size 40

> surface undust all

> ui tool show "Map Eraser"

> select add #18

211268 atoms, 225060 bonds, 4422 pseudobonds, 17444 residues, 7 models
selected  

Can only have one displayed volume when erasing  

> undo

> ui tool show "Map Eraser"

> select add #18

211268 atoms, 225060 bonds, 4422 pseudobonds, 17444 residues, 7 models
selected  

> select add #52

430586 atoms, 460206 bonds, 10242 pseudobonds, 35554 residues, 9 models
selected  

> select subtract #52

209652 atoms, 223254 bonds, 4355 pseudobonds, 17368 residues, 5 models
selected  

> select add #53

410810 atoms, 441229 bonds, 9585 pseudobonds, 33826 residues, 8 models
selected  

> select subtract #53

205848 atoms, 221047 bonds, 4355 pseudobonds, 16928 residues, 4 models
selected  

> select add #58

209136 atoms, 224719 bonds, 4513 pseudobonds, 17082 residues, 4 models
selected  

> select subtract #58

1 model selected  

Can only have one displayed volume when erasing  

[Repeated 3 time(s)]

> hide #!17 models

> hide #!16 models

> hide #!15 models

> hide #!14 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> show #!11 models

> show #!12 models

> show #!13 models

> show #!14 models

> show #!15 models

> show #!16 models

> show #!17 models

> hide #!10.2 models

> hide #!10.3 models

> show #!10.2 models

> show #!10.3 models

> hide #!10-17#!10.1-6#!11.1-5#!12.1-7#!13.1-4#!14.1-5#!15.1-7#!16.1-7#!17.1-6
> target m

> show #!10.2 models

> show #!11.2 models

> hide #!11.2 models

> show #!11.2 models

> show #!12.2 models

> show #!13.2 models

> show #!14.2 models

> show #!15.2 models

> show #!16.2 models

> show #!17.2 models

> hide #!17 models

> hide #!16 models

> hide #!15 models

> hide #!14 models

> hide #!13 models

> hide #!12 models

> hide #!11 models

> hide #!10 models

> hide #!10.2 models

> show #!10.2 models

> volume erase #10.2 center 282.93,416.04,267.14 radius 49.408

> hide #!10 models

> show #!11 models

> volume erase #11.2 center 282.93,416.04,267.14 radius 49.408

> hide #!11 models

> show #!12 models

> volume erase #12.2 center 282.93,416.04,267.14 radius 49.408

> show #!11 models

> hide #!12 models

> show #!12 models

> hide #!11 models

> show #!11 models

> hide #!12 models

> volume erase #11.2 center 282.93,416.04,267.14 radius 49.408

> hide #!11 models

> show #!12 models

> volume erase #12.2 center 282.93,416.04,267.14 radius 49.408

> hide #!12 models

> show #!13 models

> volume erase #13.2 center 282.93,416.04,267.14 radius 49.408

> hide #!13 models

> show #!14 models

> volume erase #14.2 center 282.93,416.04,267.14 radius 49.408

> hide #!14 models

> show #!15 models

> volume erase #15.2 center 282.93,416.04,267.14 radius 49.408

> hide #!15 models

> show #!16 models

> volume erase #16.2 center 282.93,416.04,267.14 radius 49.408

> hide #!16 models

> show #!17 models

> volume erase #17.2 center 282.93,416.04,267.14 radius 49.408

> show #!16 models

> show #!15 models

> show #!14 models

> show #!13 models

> show #!12 models

> show #!11 models

> show #!10 models

> surface dust #10.2 size 40

> surface dust #11.2 size 40

> surface dust #12.2 size 40

> surface dust #13.2 size 40

> surface dust #14.2 size 40

> surface dust #15.2 size 40

> surface dust #16.2 size 40

> surface dust #17.2 size 40

> surface undust all

> show #!10.3 models

> show #!10.4 models

> show #!10.5 models

> show #!10.6 models

> show #!11.3 models

> show #!11.4 models

> show #!11.5 models

> show #!12.3 models

> show #!12.4 models

> show #!12.5 models

> show #!12.6 models

> show #!12.7 models

> show #!13.3 models

> show #!13.4 models

> show #!14.3 models

> show #!14.4 models

> show #!14.5 models

> show #!15.3 models

> show #!15.5 models

> show #!15.4 models

> hide #!15.5 models

> show #!15.5 models

> hide #!15.5 models

> show #!15.5 models

> hide #!15.5 models

> show #!15.5 models

> show #!15.6 models

> show #!15.7 models

> hide #!15.5 models

> show #!16.3 models

> show #!16.4 models

> show #!16.5 models

> show #!16.6 models

> show #!16.7 models

> show #!17.3 models

> show #!17.4 models

> show #!17.5 models

> show #!17.6 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> hide #!17 models

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting flat

> lighting soft

> lighting full

> lighting soft

> graphics silhouettes true depthJump 0.01

> graphics silhouettes true depthJump 0.005

> graphics silhouettes true depthJump 0.005 width 1

> graphics silhouettes true depthJump 0.005 width 2

> surface dust #10.2 size 40

> surface dust #10.3 size 40

> surface dust #10.4 size 40

> surface dust #10.5 size 40

> surface dust #10.6 size 40

> graphics silhouettes true depthJump 0.01 width 2

> lighting full

> graphics silhouettes true depthJump 0.01 width 2

> graphics silhouettes true depthJump 0.012

> graphics silhouettes true depthJump 0.01

> lighting soft

> graphics silhouettes true depthJump 0.01

> lighting full

> graphics silhouettes true depthJump 0.02

> graphics silhouettes true depthJump 0.01

> graphics silhouettes true depthJump 0.02

> graphics silhouettes true depthJump 0.01

> graphics silhouettes true depthJump 0.01 width 1.5

> graphics silhouettes true depthJump 0.01 width 2

> graphics silhouettes true depthJump 0.01 width 1.5

[Repeated 1 time(s)]

> show #!11 models

> hide #!10 models

> show #!15 models

> hide #!15 models

> hide #!11 models

> show #!10 models

> show #!15 models

> hide #!10 models

> hide #!15 models

> show #!12 models

> hide #!12 models

> show #!11 models

> hide #!11 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!10 models

> hide #!10 models

> show #!15 models

> hide #!15 models

> show #!10 models

> hide #!10 models

> show #!12 models

> show #!10 models

> hide #!12 models

> hide #!10 models

> show #!15 models

> show #!10 models

> show #!11 models

> show #!12 models

> show #!13 models

> show #!14 models

> show #!16 models

> show #!17 models

> surface dust #10.2 size 40

> surface dust #10.3 size 40

> surface dust #10.4 size 40

> surface dust #10.5 size 40

> surface dust #10.6 size 40

> surface dust #11.2 size 40

> surface dust #11.3 size 40

> surface dust #11.4 size 40

> surface dust #11.5 size 40

> surface dust #12.2 size 40

> surface dust #12.3 size 40

> surface dust #12.4 size 40

> surface dust #12.5 size 40

> surface dust #12.6 size 40

> surface dust #12.7 size 40

> surface dust #13.2 size 40

> surface dust #13.3 size 40

> surface dust #13.4 size 40

> surface dust #14.2 size 40

> surface dust #14.3 size 40

> surface dust #14.4 size 40

> surface dust #14.5 size 40

> surface dust #15.2 size 40

> surface dust #15.3 size 40

> surface dust #15.4 size 40

> surface dust #15.6 size 40

> surface dust #15.7 size 40

> surface dust #16.2 size 40

> surface dust #16.3 size 40

> surface dust #16.4 size 40

> surface dust #16.5 size 40

> surface dust #16.6 size 40

> surface dust #16.7 size 40

> surface dust #17.2 size 40

> surface dust #17.3 size 40

> surface dust #17.4 size 40

> surface dust #17.5 size 40

> surface dust #17.6 size 40

> graphics silhouettes true depthJump 0.01 width 1.5

> surface undust all

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> hide #!17 models

> show #!17 models

> hide #!10 models

> hide #!17 models

> show #!10 models

> surface dust #10.2 size 40

> surface dust #10.3 size 40

> surface dust #10.4 size 40

> surface dust #10.5 size 40

> surface dust #10.6 size 40

> hide #!10 models

> show #!11 models

> surface dust #11.* size 10

> surface dust #11.* size 15

> surface dust #11.* size 10

> surface dust #11.* size 15

> surface dust #11.* size 20

> show #!16 models

> show #!17 models

> surface dust #11.* size 20

> surface dust all size 20

> surface undust all

> surface dust all size 20

> hide #!11 models

> show #!10 models

> hide #!16 models

> hide #!17 models

> hide #!10 models

> show #!11 models

> show #!10 models

> hide #!10 models

> hide #!11 models

> show #!12 models

> hide #!12 models

> show #!13 models

> hide #!13 models

> show #!14 models

> hide #!14 models

> show #!15 models

> hide #!15 models

> show #!16 models

> hide #!16 models

> show #!17 models

> hide #!17 models

> show #!16 models

> hide #!16 models

> show #!17 models

> hide #!17 models

> show #!16 models

> show #!15 models

> hide #!16 models

> show #!16 models

> hide #!15 models

> hide #!16 models

> show #!10 models

> save
> /Users/campbell/Desktop/Chimera_sessions/RibosomeFigures/Manuscript1/Ribofigs/PlaceholderDensitiesColoured.cxs
> includeMaps true

——— End of log from Mon Feb 9 13:25:44 2026 ———

> view name session-start

opened ChimeraX session  

> close #1-9

> hide #!10 models

> show #!50 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

> open
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/MMS_Outputs/60S_filtsharp.mrc

Opened 60S_filtsharp.mrc as #1, grid size 270,270,270, pixel 2.59, shown at
level 0.00474, step 2, values float32  

> open
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/MMS_Outputs/Decoding_filtsharp.mrc

Opened Decoding_filtsharp.mrc as #2, grid size 270,270,270, pixel 2.59, shown
at level 0.00591, step 2, values float32  

> open
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/MMS_Outputs/Hibernating_filtsharp.mrc

Opened Hibernating_filtsharp.mrc as #3, grid size 270,270,270, pixel 2.59,
shown at level 0.00507, step 2, values float32  

> open
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/MMS_Outputs/Int_Post_filtsharp.mrc

Opened Int_Post_filtsharp.mrc as #4, grid size 270,270,270, pixel 2.59, shown
at level 0.00705, step 2, values float32  

> open
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/MMS_Outputs/Post_filtsharp.mrc

Opened Post_filtsharp.mrc as #5, grid size 270,270,270, pixel 2.59, shown at
level 0.00678, step 2, values float32  

> open
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/MMS_Outputs/Rotated_filtlocal.mrc

Opened Rotated_filtlocal.mrc as #6, grid size 270,270,270, pixel 2.59, shown
at level 0.00572, step 2, values float32  

> open
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/MMS_Outputs/Translocating_filtsharp.mrc

Opened Translocating_filtsharp.mrc as #7, grid size 270,270,270, pixel 2.59,
shown at level 0.00737, step 2, values float32  

> open
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/MMS_Outputs/UnPre_cEF2_filtsharp.mrc

Opened UnPre_cEF2_filtsharp.mrc as #8, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 2, values float32  

> open
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/MMS_Outputs/UnPre_none_filtsharp.mrc

Opened UnPre_none_filtsharp.mrc as #9, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 2, values float32  

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!5 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> select add #1

2 models selected  

> select add #2

4 models selected  

> select add #3

6 models selected  

> select add #4

8 models selected  

> select add #5

10 models selected  

> select add #6

12 models selected  

> select add #7

14 models selected  

> select add #8

16 models selected  

> select add #9

18 models selected  

> show #!9 models

> show #!8 models

> show #!7 models

> show #!6 models

> show #!5 models

> show #!3 models

> show #!2 models

> show #!1 models

> ui mousemode right "translate selected models"

> view matrix models
> #1,1,0,0,-99.311,0,1,0,-92.141,0,0,1,-88.752,#2,1,0,0,-99.311,0,1,0,-92.141,0,0,1,-88.752,#3,1,0,0,-99.311,0,1,0,-92.141,0,0,1,-88.752,#4,1,0,0,-99.311,0,1,0,-92.141,0,0,1,-88.752,#5,1,0,0,-99.311,0,1,0,-92.141,0,0,1,-88.752,#6,1,0,0,-99.311,0,1,0,-92.141,0,0,1,-88.752,#7,1,0,0,-99.311,0,1,0,-92.141,0,0,1,-88.752,#8,1,0,0,-99.311,0,1,0,-92.141,0,0,1,-88.752,#9,1,0,0,-99.311,0,1,0,-92.141,0,0,1,-88.752

> view matrix models
> #1,1,0,0,-93.216,0,1,0,-92.554,0,0,1,-94.994,#2,1,0,0,-93.216,0,1,0,-92.554,0,0,1,-94.994,#3,1,0,0,-93.216,0,1,0,-92.554,0,0,1,-94.994,#4,1,0,0,-93.216,0,1,0,-92.554,0,0,1,-94.994,#5,1,0,0,-93.216,0,1,0,-92.554,0,0,1,-94.994,#6,1,0,0,-93.216,0,1,0,-92.554,0,0,1,-94.994,#7,1,0,0,-93.216,0,1,0,-92.554,0,0,1,-94.994,#8,1,0,0,-93.216,0,1,0,-92.554,0,0,1,-94.994,#9,1,0,0,-93.216,0,1,0,-92.554,0,0,1,-94.994

> fitmap #1-9 inMap #50 eachModel true

Fit map 60S_filtsharp.mrc in map Stable_60S.mrc using 24602 points  
correlation = 0.9809, correlation about mean = 0.8158, overlap = 157.4  
steps = 68, shift = 9.98, angle = 0.489 degrees  
  
Position of 60S_filtsharp.mrc (#1) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.99996477 0.00271877 0.00794088 -104.59673004  
-0.00273096 0.99999511 0.00152560 -88.45841411  
-0.00793670 -0.00154724 0.99996731 -96.64636027  
Axis -0.18005898 0.93037749 -0.31933757  
Axis point -13546.02255497 0.00000000 13851.11643574  
Rotation angle (degrees) 0.48890331  
Shift along axis -32.60332315  
  
Fit map Decoding_filtsharp.mrc in map Stable_60S.mrc using 24603 points  
correlation = 0.7661, correlation about mean = 0.3548, overlap = 146.9  
steps = 68, shift = 1.56, angle = 1.22 degrees  
  
Position of Decoding_filtsharp.mrc (#2) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.99978543 0.01842905 0.00945807 -103.58550562  
-0.01847433 0.99981818 0.00472265 -87.42783098  
-0.00936932 -0.00489637 0.99994412 -89.07491303  
Axis -0.22616677 0.44267820 -0.86768923  
Axis point -6265.48455578 4786.76384566 0.00000000  
Rotation angle (degrees) 1.21850512  
Shift along axis 62.01454742  
  
Fit map Hibernating_filtsharp.mrc in map Stable_60S.mrc using 24595 points  
correlation = 0.7787, correlation about mean = 0.3281, overlap = 134.3  
steps = 124, shift = 1.88, angle = 0.348 degrees  
  
Position of Hibernating_filtsharp.mrc (#3) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.99998606 0.00424485 0.00313938 -96.85319710  
-0.00425426 0.99998646 0.00299732 -91.34594373  
-0.00312661 -0.00301064 0.99999058 -91.62821309  
Axis -0.49453184 0.51577108 -0.69958448  
Axis point -29386.34291212 15160.94795480 0.00000000  
Rotation angle (degrees) 0.34803932  
Shift along axis 64.88506941  
  
Fit map Int_Post_filtsharp.mrc in map Stable_60S.mrc using 24597 points  
correlation = 0.7677, correlation about mean = 0.4114, overlap = 151.8  
steps = 100, shift = 1.92, angle = 0.736 degrees  
  
Position of Int_Post_filtsharp.mrc (#4) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.99992591 0.01129012 0.00455062 -99.73906411  
-0.01130875 0.99992770 0.00408847 -89.47259647  
-0.00450413 -0.00413963 0.99998129 -90.72777167  
Axis -0.32018121 0.35234943 -0.87939403  
Axis point -10451.94233830 6491.33116998 0.00000000  
Rotation angle (degrees) 0.73622044  
Shift along axis 80.19441703  
  
Fit map Post_filtsharp.mrc in map Stable_60S.mrc using 24580 points  
correlation = 0.7762, correlation about mean = 0.3382, overlap = 141.9  
steps = 68, shift = 1.44, angle = 1.09 degrees  
  
Position of Post_filtsharp.mrc (#5) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.99983572 0.01463852 0.01068893 -102.80757104  
-0.01470011 0.99987567 0.00570619 -89.10295876  
-0.01060407 -0.00586238 0.99992659 -88.56750963  
Axis -0.30401739 0.55957176 -0.77100770  
Axis point -8002.48470410 5901.46486618 0.00000000  
Rotation angle (degrees) 1.09018415  
Shift along axis 49.68202171  
  
Fit map Rotated_filtlocal.mrc in map Stable_60S.mrc using 24591 points  
correlation = 0.7945, correlation about mean = 0.3187, overlap = 116.6  
steps = 52, shift = 2.17, angle = 0.361 degrees  
  
Position of Rotated_filtlocal.mrc (#6) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.99999328 -0.00033420 -0.00364982 -93.66539986  
0.00031548 0.99998680 -0.00512742 -90.38927379  
0.00365149 0.00512624 0.99998019 -96.85802277  
Axis 0.81350364 -0.57927107 0.05154461  
Axis point 0.00000000 18523.80778301 -20933.31884960  
Rotation angle (degrees) 0.36108943  
Shift along axis -28.82976129  
  
Fit map Translocating_filtsharp.mrc in map Stable_60S.mrc using 24585 points  
correlation = 0.7526, correlation about mean = 0.4031, overlap = 145.7  
steps = 148, shift = 2.33, angle = 0.592 degrees  
  
Position of Translocating_filtsharp.mrc (#7) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.99997185 0.00183802 -0.00727434 -93.01035156  
-0.00188972 0.99997296 -0.00710675 -89.08814824  
0.00726108 0.00712029 0.99994829 -98.44500029  
Axis 0.68802502 -0.70293850 -0.18027492  
Axis point 13048.83984956 0.00000000 -14385.57490879  
Rotation angle (degrees) 0.59239406  
Shift along axis 16.37720473  
  
Fit map UnPre_cEF2_filtsharp.mrc in map Stable_60S.mrc using 24582 points  
correlation = 0.7576, correlation about mean = 0.3255, overlap = 153.5  
steps = 64, shift = 2.01, angle = 0.925 degrees  
  
Position of UnPre_cEF2_filtsharp.mrc (#8) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.99993896 0.00231071 0.01080433 -98.48723583  
-0.00243774 0.99992789 0.01175860 -94.35051032  
-0.01077638 -0.01178422 0.99987249 -86.22920269  
Axis -0.72914228 0.66837401 -0.14706368  
Axis point 0.00000000 -7149.42191612 9198.28293016  
Rotation angle (degrees) 0.92503371  
Shift along axis 21.43096244  
  
Fit map UnPre_none_filtsharp.mrc in map Stable_60S.mrc using 24588 points  
correlation = 0.7601, correlation about mean = 0.3714, overlap = 158.7  
steps = 84, shift = 1.8, angle = 0.854 degrees  
  
Position of UnPre_none_filtsharp.mrc (#9) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.99992702 0.00706930 0.00979663 -99.82492071  
-0.00715453 0.99993663 0.00869245 -92.05152250  
-0.00973456 -0.00876190 0.99991423 -87.63465742  
Axis -0.58558505 0.65526167 -0.47720257  
Axis point -7111.91642493 0.00000000 7748.31283723  
Rotation angle (degrees) 0.85393039  
Shift along axis 39.95763005  
  

> select clear

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!2 models

> show #!58 models

> hide #!50 models

Drag select of 17082 residues, 11 pseudobonds  

> select subtract #58/ET

207492 atoms, 11 pseudobonds, 17005 residues, 2 models selected  

> show #!52 models

> hide #!58 models

Drag select of 593 residues  

> show #!53 models

> hide #!52 models

Drag select of 364 residues  

> show #!52 models

> show #!58 models

> show #!2 models

> ui tool show "Color Zone"

> color zone #2 near sel distance 60

> hide #!52 models

> hide #!53 models

> hide #!58 models

> volume splitbyzone #2

Opened Decoding_filtsharp.mrc 0 as #18.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 1 as #18.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 2 as #18.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 3 as #18.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 4 as #18.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 5 as #18.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  
Opened Decoding_filtsharp.mrc 6 as #18.7, grid size 270,270,270, pixel 2.59,
shown at level 0.00591, step 1, values float32  

> hide #!18.1 models

> color #18.2 #d6d6d618 models

> color #18.2 #d6d6d61b models

> color #18.2 #d6d6d61a models

> color #18.3 #a9a9a93f models

> show #!52 models

> hide #!52 models

> show #!53 models

> volume all step 1

> show #!10 models

> hide #!10 models

> show #!2 models

> hide #!18 models

> hide #!53 models

> ui tool show "Side View"

> show #!52 models

> hide #!52 models

> show #!53 models

> select clear

Drag select of 2 Decoding_filtsharp.mrc  

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!18 models

> hide #!53 models

> hide #!18 models

> show #!3 models

> hide #!3 models

> show #!61 models

> show #!3 models

> hide #!61 models

> lighting simple

> show #!53 models

> ui tool show "Side View"

> color #3 #b2ffff73 models

> color #3 #b2ffff00 models

> color #3 #b2ffffff models

> ui tool show "Side View"

> open 6tnu1

'6tnu1' has no suffix  

> open 6tnu

6tnu title:  
Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs.
[more info...]  
  
Chain information for 6tnu #19  
---  
Chain | Description | UniProt  
2 | 18S rRNA |   
A | 40S ribosomal protein S3 | RS3_YEAST 4-225  
AA | 60S ribosomal protein L8-A | RL8A_YEAST 24-256  
AB | 60S ribosomal protein L23-A | RL23A_YEAST 2-137  
AC | 60S ribosomal protein L36-A | RL36A_YEAST 2-100  
AD | 60S ribosomal protein L9-A | RL9A_YEAST 1-191  
AE | 60S ribosomal protein L24-A | RL24A_YEAST 1-126  
AF | 60S ribosomal protein L37-A | RL37A_YEAST 2-82  
AG | 60S ribosomal protein L11-B | RL11B_YEAST 6-174  
AH | 60S ribosomal protein L25 | RL25_YEAST 22-142  
AI | 60S ribosomal protein L38 | RL38_YEAST 2-78  
AJ | 60S ribosomal protein L13-A | RL13A_YEAST 2-194  
AK | 60S ribosomal protein L26-A | RL26A_YEAST 2-126  
AL | 60S ribosomal protein L39 | RL39_YEAST 2-51  
AM | 60S ribosomal protein L14-A | RL14A_YEAST 3-138  
AN | 60S ribosomal protein L27-A | RL27A_YEAST 2-136  
AO | Ubiquitin-60S ribosomal protein L40 | RL40A_YEAST 77-128  
AP | 60S ribosomal protein L42-A | RL44A_YEAST 2-104  
AQ | 60S ribosomal protein L15-A | RL15A_YEAST 2-204  
AR | 60S ribosomal protein L28 | RL28_YEAST 2-149  
AS | 60S ribosomal protein L41-A |   
AT | 60S ribosomal protein L43-A | RL43A_YEAST 2-92  
AU | 60S ribosomal protein L16-A | RL16A_YEAST 3-199  
AV | 60S ribosomal protein L29 | RL29_YEAST 2-59  
AW | 60S ribosomal protein L2-A | RL2A_YEAST 2-252  
AX | 60S ribosomal protein L17-A | RL17A_YEAST 2-184  
AY | 60S ribosomal protein L30 | RL30_YEAST 9-104  
B | Rps5p | A0A1L4AA68_YEASX 20-225  
BA | 60S ribosomal protein L3 | RL3_YEAST 2-387  
BB | 60S ribosomal protein L18-A | RL18A_YEAST 2-186  
BC | 60S ribosomal protein L31-A | RL31A_YEAST 4-112  
BD | 60S ribosomal protein L10 | RL10_YEAST 2-219  
BE | 60S ribosomal protein L4-A | RL4A_YEAST 2-362  
BF | 60S ribosomal protein L19-A | RL19A_YEAST 2-189  
BG | 60S ribosomal protein L32 | RL32_YEAST 2-128  
BH | 60S ribosomal protein L20-A | RL20A_YEAST 2-172  
BI | 60S ribosomal protein L5 | RL5_YEAST 4-297  
BJ | 60S ribosomal protein L21-A | RL21A_YEAST 2-160  
BK | 60S ribosomal protein L33-A | RL33A_YEAST 2-107  
BL | 60S ribosomal protein L22-A | RL22A_YEAST 9-108  
BM | 60S ribosomal protein L6-B | RL6B_YEAST 2-176  
BN | 60S ribosomal protein L34-A | RL34A_YEAST 2-113  
BO | 60S ribosomal protein L7-A | RL7A_YEAST 23-244  
BP | 60S ribosomal protein L35-A | RL35A_YEAST 2-120  
BQ | 25S rRNA |   
BR | 5S rRNA |   
BS | 5.8S rRNA |   
BT | 60S ribosomal protein L1 |   
C | 40S ribosomal protein S10-A | RS10A_YEAST 1-92  
D | 40S ribosomal protein S12 | RS12_YEAST 23-143  
E | 40S ribosomal protein S15 | RS15_YEAST 13-129  
F | 40S ribosomal protein S16-A | RS16A_YEAST 3-143  
G | 40S ribosomal protein S17-B | RS17B_YEAST 2-126  
H | 40S ribosomal protein S18-A | RS18A_YEAST 2-146  
I | 40S ribosomal protein S19-A | RS19A_YEAST 2-144  
J | 40S ribosomal protein S20 | RS20_YEAST 20-119  
K | 40S ribosomal protein S25-A | RS25A_YEAST 24-105  
L | 40S ribosomal protein S28-A | RS28A_YEAST 5-67  
M | 40S ribosomal protein S29-A | RS29A_YEAST 4-56  
N | Ubiquitin-40S ribosomal protein S31 | RS31_YEAST 80-152  
O | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 5-316  
P | 40S ribosomal protein S0-A | RSSA1_YEAS1 2-207  
Q | 40S ribosomal protein S1-A | RS3A1_YEAS1 2-233  
R | 40S ribosomal protein S2 | RS2_YEAST 34-249  
S | 40S ribosomal protein S4-A | RS4A_YEAST 2-259  
T | 40S ribosomal protein S6-A | RS6A_YEAST 1-228  
U | 40S ribosomal protein S7-A | RS7A_YEAST 4-187  
V | 40S ribosomal protein S8 | A0A0J9X221_LACKL 2-199  
W | 40S ribosomal protein S9-A | RS9A_YEAST 2-185  
X | 40S ribosomal protein S11-A | RS11A_YEAST 4-145  
Y | 40S ribosomal protein S13 | RS13_YEAST 2-151  
Z | 40S ribosomal protein S14-B | RS14B_YEAST 11-137  
a | 40S ribosomal protein S21-A | RS21A_YEAST 1-87  
b | 40S ribosomal protein S22-A | RS22A_YEAST 2-130  
c | 40S ribosomal protein S23-A | RS23A_YEAST 2-145  
d | 40S ribosomal protein S24-A | RS24A_YEAST 2-135  
e | 40S ribosomal protein S26-B | RS26B_YEAST 2-98  
eI | Eukaryotic translation initiation factor 5A-1 | IF5A1_YEAST 4-157  
f | 40S ribosomal protein S27-A | RS27A_YEAST 2-82  
g | 40S ribosomal protein S30-A | RS30A_YEAST 2-61  
l | mRNA |   
m | A-site tRNA |   
n | P-site tRNA |   
  
Non-standard residues in 6tnu #19  
---  
3HE —
4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
ZN — zinc ion  
  
1555 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select #19/2:1362@OP2

1 atom, 1 residue, 1 model selected  

> view matrix models #19,1,0,0,-221.3,0,1,0,194.79,0,0,1,143.1

> view matrix models
> #19,0.26444,-0.84282,-0.46875,307.63,-0.43264,-0.53808,0.72339,536.83,-0.86191,0.011508,-0.50693,733.24

> view matrix models
> #19,0.00473,-0.38475,0.92301,-101.5,0.74793,0.61403,0.25212,49.733,-0.66376,0.68916,0.29067,300.09

> view matrix models
> #19,0.46851,0.1293,0.87394,-343.68,0.33944,0.88695,-0.3132,219.63,-0.81564,0.44339,0.37166,384.03

> open 6y0u

Summary of feedback from opening 6y0u fetched from pdb  
---  
notes | Fetching compressed mmCIF 6y0u from http://files.rcsb.org/download/6y0u.cif  
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif  
Fetching CCD DLY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/DLY/DLY.cif  
Fetching CCD O65 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/5/O65/O65.cif  
Fetching CCD ZDC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/ZDC/ZDC.cif  
  
6y0u title:  
Fucosylated Bicyclic peptide bp71 bound to the fucose binding lectin LecB PA-
IIL from Pseudomonas aeruginosa at 1.5 Angstrom resolution [more info...]  
  
Chain information for 6y0u #20  
---  
Chain | Description | UniProt  
A B C D | Fucose-binding lectin | A0A069Q9V4_PSEAI 0-114  
E F H | bp71 |   
  
Non-standard residues in 6y0u #20  
---  
CA — calcium ion  
NH2 — amino group  
O65 — 3,5-bis(hydroxymethyl)-4-methyl-benzaldehyde  
ZDC — 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid  
  

> hide #!19 models

> hide #!20 models

> show #!20 models

> hide #!3 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> show #!20 target m

> view #20 clip false

> close #20

> show #!2 models

> view #2 clip false

> hide #!2 models

> close #19

> open 8y0u

8y0u title:  
dormant ribosome with STM1 [more info...]  
  
Chain information for 8y0u #19  
---  
Chain | Description | UniProt  
5 | Eukaryotic translation initiation factor 5A-1 | IF5A1_YEAST 1-157  
C1 | 25S rRNA |   
C2 | 18S rRNA |   
C3 | 5.8S rRNA |   
C4 | 5S rRNA |   
LA | Large ribosomal subunit protein uL2A | RL2A_YEAST 1-254  
LB | Large ribosomal subunit protein uL3 | RL3_YEAST 1-387  
LC | Large ribosomal subunit protein uL4A | RL4A_YEAST 1-362  
LD | Large ribosomal subunit protein uL18 | RL5_YEAST 1-297  
LE | Large ribosomal subunit protein eL6B | RL6B_YEAST 1-176  
LF | Large ribosomal subunit protein uL30A | RL7A_YEAST 1-244  
LG | Large ribosomal subunit protein eL8A | RL8A_YEAST 1-256  
LH | Large ribosomal subunit protein uL6A | RL9A_YEAST 1-191  
LI | Large ribosomal subunit protein uL16 | RL10_YEAST 1-221  
LJ | Large ribosomal subunit protein uL5B | RL11B_YEAST 1-174  
LL | Large ribosomal subunit protein eL13A | RL13A_YEAST 1-199  
LM | Large ribosomal subunit protein eL14A | RL14A_YEAST 1-138  
LN | Large ribosomal subunit protein eL15A | RL15A_YEAST 1-204  
LO | Large ribosomal subunit protein uL13A | RL16A_YEAST 1-199  
LP | Large ribosomal subunit protein uL22A | RL17A_YEAST 1-184  
LQ | Large ribosomal subunit protein eL18A | RL18A_YEAST 1-186  
LR | Large ribosomal subunit protein eL19A | RL19A_YEAST 1-189  
LS | Large ribosomal subunit protein eL20A | RL20A_YEAST 1-172  
LT | Large ribosomal subunit protein eL21A | RL21A_YEAST 1-160  
LU | Large ribosomal subunit protein eL22A | RL22A_YEAST 1-121  
LV | Large ribosomal subunit protein uL14A | RL23A_YEAST 1-137  
LW | Large ribosomal subunit protein eL24A | RL24A_YEAST 1-155  
LX | Large ribosomal subunit protein uL23 | RL25_YEAST 1-142  
LY | Large ribosomal subunit protein uL24A | RL26A_YEAST 1-127  
LZ | Large ribosomal subunit protein eL27A | RL27A_YEAST 1-136  
La | Large ribosomal subunit protein uL15 | RL28_YEAST 1-149  
Lb | Large ribosomal subunit protein eL29 | RL29_YEAST 1-59  
Lc | Large ribosomal subunit protein eL30 | RL30_YEAST 1-105  
Ld | Large ribosomal subunit protein eL31A | RL31A_YEAST 1-113  
Le | Large ribosomal subunit protein eL32 | RL32_YEAST 1-130  
Lf | Large ribosomal subunit protein eL33A | RL33A_YEAST 1-107  
Lg | Large ribosomal subunit protein eL34A | RL34A_YEAST 1-121  
Lh | Large ribosomal subunit protein uL29A | RL35A_YEAST 1-120  
Li | Large ribosomal subunit protein eL36A | RL36A_YEAST 1-100  
Lj | Large ribosomal subunit protein eL37A | RL37A_YEAST 1-88  
Lk | Large ribosomal subunit protein eL38 | RL38_YEAST 1-78  
Ll | Large ribosomal subunit protein eL39 | RL39_YEAST 2-51  
Lm | Ubiquitin-ribosomal protein eL40A fusion protein | RL40A_YEAST 1-128  
Ln | Large ribosomal subunit protein eL41A | RL41A_YEAST 1-25  
Lo | Large ribosomal subunit protein eL42A | RL44A_YEAST 1-106  
Lp | Large ribosomal subunit protein eL43A | RL43A_YEAST 1-92  
P0 | Large ribosomal subunit protein uL10 | RLA0_YEAST 1-312  
P2 | Large ribosomal subunit protein uL11A | RL12A_YEAST 1-165  
SA | Small ribosomal subunit protein uS2A | RSSA1_YEAST 1-252  
SB | 40S ribosomal protein S1-A | RS3A1_YEAST 1-255  
SC | 40S ribosomal protein S2 | RS2_YEAST 1-254  
SE | 40S ribosomal protein S4-A | RS4A_YEAST 1-261  
SG | 40S ribosomal protein S6-A | RS6A_YEAST 1-236  
SH | 40S ribosomal protein S7-A | RS7A_YEAST 1-190  
SI | 40S ribosomal protein S8-A | RS8A_YEAST 1-200  
SJ | 40S ribosomal protein S9-A | RS9A_YEAST 1-197  
SK | Small ribosomal subunit protein eS10A | RS10A_YEAST 1-105  
SL | Small ribosomal subunit protein uS17A | RS11A_YEAST 1-156  
SM | Small ribosomal subunit protein eS12 | RS12_YEAST 1-143  
SN | 40S ribosomal protein S13 | RS13_YEAST 1-151  
SO | Small ribosomal subunit protein uS11B | RS14B_YEAST 0-137  
SP | Small ribosomal subunit protein uS19 | RS15_YEAST 1-142  
SQ | Small ribosomal subunit protein uS9A | RS16A_YEAST 1-143  
ST | Small ribosomal subunit protein eS19A | RS19A_YEAST 1-144  
SU | Small ribosomal subunit protein uS10 | RS20_YEAST 1-121  
SV | Small ribosomal subunit protein eS21A | RS21A_YEAST 1-87  
SW | 40S ribosomal protein S22-A | RS22A_YEAST 1-130  
SX | 40S ribosomal protein S23-A | RS23A_YEAST 1-145  
SY | 40S ribosomal protein S24-A | RS24A_YEAST 1-135  
SZ | Small ribosomal subunit protein eS25A | RS25A_YEAST 1-108  
Sa | Small ribosomal subunit protein eS26B | RS26B_YEAST 1-119  
Sb | 40S ribosomal protein S27-A | RS27A_YEAST 1-82  
Sc | Small ribosomal subunit protein eS28A | RS28A_YEAST 1-67  
Sd | Small ribosomal subunit protein uS14A | RS29A_YEAST 1-56  
Se | 40S ribosomal protein S30-A | RS30A_YEAST 1-63  
Sf | Ubiquitin-ribosomal protein eS31 fusion protein | RS31_YEAST 1-152  
s | Suppressor protein STM1 | STM1_YEAST 1-269  
  
Non-standard residues in 8y0u #19  
---  
MG — magnesium ion  
ZN — zinc ion  
  
1555 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select #19/LD:220@CB

1 atom, 1 residue, 1 model selected  

> view matrix models #19,1,0,0,-25.95,0,1,0,-120.45,0,0,1,6.1048

> view matrix models
> #19,0.56606,-0.10375,-0.81781,301.88,-0.74699,-0.48418,-0.45561,520.07,-0.34869,0.8688,-0.35157,213.97

> view matrix models
> #19,0.85301,0.19024,-0.48599,82.735,-0.21215,-0.7244,-0.65593,493.57,-0.47683,0.66261,-0.57756,347.24

> view matrix models
> #19,0.85301,0.19024,-0.48599,71.494,-0.21215,-0.7244,-0.65593,403.62,-0.47683,0.66261,-0.57756,393.35

> select add #19

196269 atoms, 210786 bonds, 5371 pseudobonds, 16186 residues, 4 models
selected  

> select clear

> select add #19

196269 atoms, 210786 bonds, 5371 pseudobonds, 16186 residues, 4 models
selected  

> hide sel atoms

> show sel cartoons

> hide #!53 models

> show #!50 models

> view matrix models
> #19,0.85301,0.19024,-0.48599,118.68,-0.21215,-0.7244,-0.65593,629.5,-0.47683,0.66261,-0.57756,374.33

> view matrix models
> #19,0.61593,-0.028922,-0.78727,301.45,-0.55994,-0.71903,-0.41166,655.05,-0.55417,0.69437,-0.45907,357.33

> view matrix models
> #19,0.62051,0.067521,-0.78129,276.21,-0.67642,-0.45799,-0.5768,662.31,-0.39677,0.88639,-0.23852,220.09

> view matrix models
> #19,0.62051,0.067521,-0.78129,273.41,-0.67642,-0.45799,-0.5768,663.53,-0.39677,0.88639,-0.23852,204.39

> fitmap #19 inMap #50

Fit molecule 8y0u (#19) to map Stable_60S.mrc (#50) using 196269 atoms  
average map value = 0.5701, steps = 116  
shifted from previous position = 14.3  
rotated from previous position = 17.6 degrees  
atoms outside contour = 82391, contour level = 0.6  
  
Position of 8y0u (#19) relative to Stable_60S.mrc (#50) coordinates:  
Matrix rotation and translation  
0.47892449 0.28157152 -0.83147387 260.86164343  
-0.59542167 -0.59179828 -0.54336712 662.20184423  
-0.64506151 0.75530938 -0.11577290 258.01173204  
Axis 0.82293219 -0.11812390 -0.55572417  
Axis point 0.00000000 274.34385547 413.50076861  
Rotation angle (degrees) 127.90277011  
Shift along axis -6.93377515  
  

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> rename #19 Stm1

> select #19/s:130

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

> select up

75 atoms, 74 bonds, 15 residues, 1 model selected  

> select up

104 atoms, 103 bonds, 21 residues, 1 model selected  

> select up

137 atoms, 135 bonds, 26 residues, 1 model selected  

> select up

261 atoms, 261 bonds, 42 residues, 1 model selected  

> select up

196269 atoms, 210786 bonds, 16186 residues, 1 model selected  

> select down

261 atoms, 261 bonds, 42 residues, 1 model selected  

> select ~sel & ##selected

196008 atoms, 210525 bonds, 5370 pseudobonds, 16144 residues, 4 models
selected  

> hide sel cartoons

> select clear

> show #!61 models

> hide #!61 models

> hide #!19 models

> hide #!50 models

> show #!10 models

> show #!11 models

> show #!12 models

> show #!13 models

> show #!14 models

> show #!15 models

> show #!16 models

> show #!17 models

> hide #!17 models

> hide #!16 models

> hide #!15 models

> hide #!14 models

> show #!14 models

> hide #!13 models

> hide #!14 models

> hide #!12 models

> hide #!11 models

> hide #!10 models

> color #19 #d783ffff

> show #!19 models

> color #19 #9437ffff

> show #!3 models

> hide #!3 models

> show #!61 models

> show #!52 models

> hide #!52 models

> show #!53 models

> hide #!61 models

> hide #!19 models

> show #!19 models

> show #!61 models

> hide #!53 models

> show #!53 models

Drag select of 17577 residues, 29 pseudobonds  

> select subtract #53/m

208981 atoms, 29 pseudobonds, 17501 residues, 5 models selected  

> select subtract #61/ASIT

207345 atoms, 29 pseudobonds, 17425 residues, 5 models selected  

> select subtract #61/PSIT

205701 atoms, 29 pseudobonds, 17348 residues, 5 models selected  

> show #!3 models

> color zone #3 near sel distance 60

> volume splitbyzone #3

Opened Hibernating_filtsharp.mrc 0 as #20.1, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 1 as #20.2, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 2 as #20.3, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 3 as #20.4, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 4 as #20.5, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  
Opened Hibernating_filtsharp.mrc 5 as #20.6, grid size 270,270,270, pixel
2.59, shown at level 0.00507, step 1, values float32  

> hide #!19 models

> rename #19 id #60

> hide #!61 models

> hide #!53 models

> hide #!20.1 models

> color #20.2 #d6d6d61a models

> color #20.3 #a9a9a93f models

> hide #!20 models

> show #!4 models

> show #!3 models

> hide #!3 models

> show #!61 models

> hide #!4 models

Drag select of 17095 residues, 28 pseudobonds  

> show #!4 models

> color zone #4 near sel distance 60

> hide #!4 models

> show #!4 models

> show #!53 models

> hide #!53 models

> hide #!4 models

> show #!53 models

> hide #!53 models

> show #!52 models

> select add #61

207066 atoms, 221714 bonds, 5069 pseudobonds, 17603 residues, 4 models
selected  

> select subtract #61

Nothing selected  

> hide #!61 models

> show #!53 models

> hide #!53 models

> select add #52

220934 atoms, 236952 bonds, 5887 pseudobonds, 18186 residues, 4 models
selected  

> show sel atoms

> hide sel atoms

> select clear

> show #!58 models

> hide #!58 models

> show #!4 models

> hide #!52 models

> show #!61 models

> hide #!4 models

Drag select of 17095 residues, 28 pseudobonds  

> show #!60 models

> hide #!61 models

> hide #!60 models

> show #!58 models

Drag select of 148 residues  

> select clear

Drag select of 351 residues  

> select (sel & #58/2S)

1332 atoms, 1490 bonds, 13 pseudobonds, 62 residues, 2 models selected  

> select add #58/L1

2941 atoms, 3124 bonds, 13 pseudobonds, 266 residues, 2 models selected  

> hide #!58 models

> show #!61 models

Drag select of 17095 residues, 28 pseudobonds  

> show #!58 models

> hide #!58 models

> show #!60 models

> hide #!61 models

Drag select of 42 residues, 1 pseudobonds  

> show #!4 models

> color zone #4 near sel distance 60

> show #!3 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> show #!61 models

> hide #!3 models

> show #!59 models

> hide #!61 models

> hide #!60 models

> show #!61 models

> select clear

Drag select of 121 residues  

> select clear

> hide #!61 models

> show #!61 models

> hide #!59 models

> show #!59 models

> hide #!59 models

> show #!59 models

> hide #!59 models

> show #!59 models

> hide #!59 models

> show #!59 models

> hide #!59 models

> show #!59 models

> hide #!59 models

> show #!59 models

> hide #!61 models

> hide #!59 models

> show #!4 models

> hide #!4 models

> show #!2 models

> show #!58 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!61 models

> hide #!61 models

> hide #!2 models

> hide #!58 models

> show #!59 models

> show #!12 models

> hide #!59 models

> show #!59 models

> hide #!12 models

> show #!4 models

> hide #!4 models

> hide #!59 models

> show #!61 models

Drag select of 17095 residues, 28 pseudobonds  
[Repeated 1 time(s)]

> show #!58 models

> hide #!61 models

Drag select of 752 residues  

> select (sel & #58/2S)

3065 atoms, 3416 bonds, 65 pseudobonds, 144 residues, 2 models selected  

> select clear

Drag select of 838 residues  

> select (sel & #58/2S)

1096 atoms, 1226 bonds, 12 pseudobonds, 51 residues, 2 models selected  
Drag select of 1057 residues  

> select (sel & #58/2S)

1118 atoms, 1252 bonds, 12 pseudobonds, 52 residues, 2 models selected  

> select add #58/L1

2727 atoms, 2886 bonds, 12 pseudobonds, 256 residues, 2 models selected  

> hide #!58 models

> show #!61 models

Drag select of 17095 residues, 28 pseudobonds  

> show #!4 models

> color zone #4 near sel distance 60

> volume splitbyzone #4

Opened Int_Post_filtsharp.mrc 0 as #19.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 1 as #19.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 2 as #19.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 3 as #19.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 4 as #19.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  
Opened Int_Post_filtsharp.mrc 5 as #19.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00705, step 1, values float32  

> hide #!19.1 models

> hide #!61 models

> color #19.2 #d6d6d619 models

> color #19.3 #a9a9a940 models

> hide #!19 models

> show #!5 models

> show #!58 models

> hide #!5 models

Drag select of 17082 residues, 11 pseudobonds  

> show #!5 models

> hide #!58 models

> show #!58 models

> select subtract #58/ET

207492 atoms, 11 pseudobonds, 17005 residues, 2 models selected  

> color zone #5 near sel distance 60

> show #!4 models

> hide #!4 models

> select #58/ET:45

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

> select up

1644 atoms, 1836 bonds, 77 residues, 1 model selected  

> color sel #d6d6d6ff

> hide #!5 models

Drag select of 17082 residues, 11 pseudobonds  

> show #!5 models

> color zone #5 near sel distance 60

> volume splitbyzone #5

Opened Post_filtsharp.mrc 0 as #21.1, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Post_filtsharp.mrc 1 as #21.2, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Post_filtsharp.mrc 2 as #21.3, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  
Opened Post_filtsharp.mrc 3 as #21.4, grid size 270,270,270, pixel 2.59, shown
at level 0.00678, step 1, values float32  

> hide #!21.1 models

> hide #!58 models

> color #21.2 #d6d6d619 models

> color #21.3 #a9a9a93f models

> hide #!21 models

> show #!6 models

> show #!5 models

> hide #!6 models

> show #!6 models

> hide #!5 models

> show #!59 models

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/BfactorScreener/20260216_MMS_Rotated_Bfactorscreening/LocRes_Bfac_-100_locres.mrc

Opened LocRes_Bfac_-100_locres.mrc as #22, grid size 270,270,270, pixel 2.59,
shown at level 50, step 2, values float32  

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/BfactorScreener/20260216_MMS_Rotated_Bfactorscreening/LocRes_Bfac_-200_locres.mrc

Opened LocRes_Bfac_-200_locres.mrc as #23, grid size 270,270,270, pixel 2.59,
shown at level 50, step 2, values float32  

> hide #!6 models

> hide #!59 models

> hide #!23 models

> show #!23 models

> volume #23 level 32.75

> volume #23 level 23.19

> volume #23 step 1

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/BfactorScreener/20260216_MMS_Rotated_Bfactorscreening/LocRes_Bfac_-200_locres_filtered.mrc

Opened LocRes_Bfac_-200_locres_filtered.mrc as #24, grid size 270,270,270,
pixel 2.59, shown at level 0.0133, step 2, values float32  

> hide #!23 models

> hide #!22 models

> close #22-23

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/BfactorScreener/20260216_MMS_Rotated_Bfactorscreening/LocRes_Bfac_-100_locres_filtered.mrc

Opened LocRes_Bfac_-100_locres_filtered.mrc as #22, grid size 270,270,270,
pixel 2.59, shown at level 0.0133, step 2, values float32  

> hide #!22 models

> hide #!24 models

> show #!22 models

> show #!24 models

> hide #!24 models

> volume #24 step 1

> volume #22 step 1

> show #!24 models

> hide #!22 models

> show #!22 models

> hide #!24 models

> show #!24 models

> hide #!22 models

> show #!22 models

> tile

2 models tiled  

> show #!6 models

> close #22,24

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> hide #!6 models

> show #!6 models

> show #!7 models

> hide #!7 models

> hide #!6 models

> show #!6 models

> show #!50 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> fitmap #6 inMap #50

Fit map Rotated_filtlocal.mrc in map Stable_60S.mrc using 196492 points  
correlation = 0.7434, correlation about mean = 0.1434, overlap = 738.7  
steps = 236, shift = 29.4, angle = 33.5 degrees  
  
Position of Rotated_filtlocal.mrc (#6) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.40558707 0.79658660 0.44827327 -320.07103706  
-0.76555288 0.56399683 -0.30957449 424.14795406  
-0.49942759 -0.21761748 0.83857899 181.34646724  
Axis 0.05026495 0.51802614 -0.85388662  
Axis point 203.82100972 556.97259991 0.00000000  
Rotation angle (degrees) 66.16642127  
Shift along axis 48.78205109  
  

> select #6

2 models selected  

> view matrix models
> #6,0.40559,0.79659,0.44827,-349.57,-0.76555,0.564,-0.30957,358.75,-0.49943,-0.21762,0.83858,190.05

> view matrix models
> #6,0.94014,-0.23767,-0.24422,65.746,0.20526,0.967,-0.15092,-182.68,0.27203,0.091758,0.9579,-234.03

> view matrix models
> #6,0.92573,-0.35085,-0.14118,72.909,0.35425,0.93515,-0.0010605,-278.53,0.1324,-0.049033,0.98998,-147.3

> view matrix models
> #6,0.92573,-0.35085,-0.14118,122.49,0.35425,0.93515,-0.0010605,-205.56,0.1324,-0.049033,0.98998,-132.55

> view matrix models
> #6,0.92573,-0.35085,-0.14118,91.802,0.35425,0.93515,-0.0010605,-195.22,0.1324,-0.049033,0.98998,-109.22

> view matrix models
> #6,0.98533,-0.087152,-0.14673,-18.377,0.10608,0.98627,0.12653,-170.38,0.13369,-0.14024,0.98105,-75.003

> fitmap #6 inMap #50

Fit map Rotated_filtlocal.mrc in map Stable_60S.mrc using 196492 points  
correlation = 0.7944, correlation about mean = 0.3224, overlap = 931.5  
steps = 96, shift = 13.8, angle = 12.5 degrees  
  
Position of Rotated_filtlocal.mrc (#6) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.99999303 -0.00001062 -0.00373347 -93.78127722  
-0.00000839 0.99998703 -0.00509241 -90.26036119  
0.00373347 0.00509240 0.99998006 -96.84468934  
Axis 0.80647742 -0.59126487 0.00017675  
Axis point 0.00000000 18937.00948113 -20359.79935284  
Rotation angle (degrees) 0.36178966  
Shift along axis -22.28181842  
  

> select clear

> hide #!50 models

> show #!59 models

> hide #!6 models

> show #!51 models

Drag select of 17213 residues, 12 pseudobonds  

> color zone #6 near sel distance 60

> hide #!59 models

> hide #!51 models

> show #!6 models

> volume splitbyzone #6

Opened Rotated_filtlocal.mrc 0 as #22.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 1 as #22.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 2 as #22.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 3 as #22.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  
Opened Rotated_filtlocal.mrc 4 as #22.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00572, step 1, values float32  

> hide #!22.1 models

> color #22.2 #d6d6d614 models

> color #22.2 #d6d6d61b models

> color #22.3 #a9a9a93f models

> hide #!22 models

> show #!7 models

> hide #!7 models

> show #!51 models

> show #!59 models

> hide #!51 models

> hide #!59 models

> show #!51 models

> show #!59 models

> hide #!51 models

> hide #!59 models

> show #!51 models

> show #!59 models

> hide #!51 models

> hide #!59 models

> show #!59 models

> show #!51 models

> hide #!59 models

> hide #!51 models

> show #!7 models

> hide #!7 models

> show #!51 models

> show #!59 models

> hide #!51 models

> hide #!59 models

> show #!61 models

> show #!51 models

Drag select of 5116 residues, 14 pseudobonds  
Drag select of 5449 residues, 14 pseudobonds  

> hide #!61 models

> show #!61 models

Drag select of 2400 residues, 8 pseudobonds  
Drag select of 3586 residues, 10 pseudobonds  
Drag select of 4530 residues, 10 pseudobonds  

> select (sel & #61/eEF2)

6066 atoms, 6176 bonds, 781 residues, 1 model selected  

> hide #!61 models

Drag select of 149 residues  

> hide #!51 models

> show #!59 models

Drag select of 17064 residues, 12 pseudobonds  

> show #!7 models

> hide #!59 models

> color zone #7 near sel distance 60

> volume splitbyzone #7

Opened Translocating_filtsharp.mrc 0 as #23.1, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 1 as #23.2, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 2 as #23.3, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 3 as #23.4, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 4 as #23.5, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  
Opened Translocating_filtsharp.mrc 5 as #23.6, grid size 270,270,270, pixel
2.59, shown at level 0.00737, step 1, values float32  

> hide #!23.1 models

> color #23.2 #d6d6d61a models

> color #23.3 #a9a9a940 models

> show #!6 models

> hide #!6 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!23 models

> show #!23 models

> hide #!20 models

> show #!20 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> hide #!20 models

> show #!23 models

> hide #!23 models

> show #!8 models

> show #!58 models

> hide #!8 models

Drag select of 17082 residues, 11 pseudobonds  

> select subtract #58/Et)

Expected an objects specifier or a keyword  

> select subtract #58/ET

207492 atoms, 11 pseudobonds, 17005 residues, 2 models selected  

> hide #!58 models

> show #!53 models

Drag select of 440 residues  

> show #!58 models

> hide #!53 models

> hide #!58 models

> show #!8 models

> show #!61 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

Drag select of 3691 residues, 8 pseudobonds, 8 UnPre_cEF2_filtsharp.mrc  

> hide #!8 models

> select subtract #8

43527 atoms, 8 pseudobonds, 3691 residues, 2 models selected  

> select (sel & #61/eEF2)

4841 atoms, 4922 bonds, 624 residues, 1 model selected  

> hide #!61 models

> show #!58 models

Drag select of 17082 residues, 11 pseudobonds  

> select subtract #58/ET

212333 atoms, 4922 bonds, 11 pseudobonds, 17629 residues, 3 models selected  

> hide #!58 models

> show #!52 models

> hide #!52 models

> show #!53 models

Drag select of 440 residues  

> show #!58 models

> show #!61 models

> show #!8 models

> color zone #8 near sel distance 60

> hide #!61 models

> hide #!58 models

> hide #!53 models

> show #!16 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!16 models

> open 8xu8

Summary of feedback from opening 8xu8 fetched from pdb  
---  
note | Fetching compressed mmCIF 8xu8 from http://files.rcsb.org/download/8xu8.cif  
  
8xu8 title:  
State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during
peptidyl transferation [more info...]  
  
Chain information for 8xu8 #24  
---  
Chain | Description | UniProt  
2 | 18S rRNA |   
A | 25S rRNA |   
B | 5S rRNA |   
C | 5.8S rRNA |   
D | Large ribosomal subunit protein uL2A | RL2A_YEAST 2-252  
E | Large ribosomal subunit protein uL3 | RL3_YEAST 2-387  
F | Large ribosomal subunit protein uL4A | RL4A_YEAST 2-362  
G | Large ribosomal subunit protein uL18 | RL5_YEAST 4-297  
H | Large ribosomal subunit protein eL6B | RL6B_YEAST 2-176  
I | Large ribosomal subunit protein uL30A | RL7A_YEAST 23-244  
J | Large ribosomal subunit protein eL8A | RL8A_YEAST 24-256  
K | Large ribosomal subunit protein uL6A | RL9A_YEAST 1-191  
L | Large ribosomal subunit protein uL16 | RL10_YEAST 2-219  
M | Large ribosomal subunit protein uL5B | RL11B_YEAST 6-174  
N | Large ribosomal subunit protein eL13A | RL13A_YEAST 2-194  
O | Large ribosomal subunit protein eL14A | RL14A_YEAST 3-138  
P | Large ribosomal subunit protein eL15A | RL15A_YEAST 2-204  
Q | Large ribosomal subunit protein uL13A | RL16A_YEAST 3-199  
R | Large ribosomal subunit protein uL22A | RL17A_YEAST 2-184  
S | Large ribosomal subunit protein eL18A | RL18A_YEAST 2-186  
SA | Small ribosomal subunit protein uS3 | RS3_YEAST 4-225  
SB | Small ribosomal subunit protein uS7 | RS5_YEAST 20-225  
SC | Small ribosomal subunit protein eS10A | RS10A_YEAST 1-92  
SD | Small ribosomal subunit protein eS12 | RS12_YEAST 23-143  
SE | Small ribosomal subunit protein uS19 | RS15_YEAST 13-129  
SF | Small ribosomal subunit protein uS9A | RS16A_YEAST 3-143  
SG | Small ribosomal subunit protein eS17A | RS17A_YEAST 2-122  
SH | Small ribosomal subunit protein uS13A | RS18A_YEAST 2-146  
SI | Small ribosomal subunit protein eS19A | RS19A_YEAST 2-144  
SJ | Small ribosomal subunit protein uS10 | RS20_YEAST 20-119  
SK | Small ribosomal subunit protein eS25A | RS25A_YEAST 1-108  
SL | Small ribosomal subunit protein eS28A | RS28A_YEAST 5-67  
SM | Small ribosomal subunit protein uS14A | RS29A_YEAST 4-56  
SN | Small ribosomal subunit protein eS31 | RS31_YEAST 80-152  
SO | Small ribosomal subunit protein RACK1 | GBLP_YEAST 5-316  
SP | Small ribosomal subunit protein uS2A | RSSA1_YEAST 2-207  
SQ | Small ribosomal subunit protein eS1A | RS3A1_YEAST 2-233  
SR | Small ribosomal subunit protein uS5 | RS2_YEAST 34-249  
SS | Small ribosomal subunit protein eS4A | RS4A_YEAST 2-259  
ST | Small ribosomal subunit protein eS6A | RS6A_YEAST 1-228  
SU | Small ribosomal subunit protein eS7A | RS7A_YEAST 4-187  
SV | Small ribosomal subunit protein eS8A | RS8A_YEAST 2-199  
SW | Small ribosomal subunit protein uS4A | RS9A_YEAST 2-185  
SX | Small ribosomal subunit protein uS17A | RS11A_YEAST 4-145  
SY | Small ribosomal subunit protein uS15 | RS13_YEAST 2-151  
SZ | Small ribosomal subunit protein uS11B | RS14B_YEAST 11-137  
Sa | Small ribosomal subunit protein eS21A | RS21A_YEAST 1-87  
Sb | Small ribosomal subunit protein uS8A | RS22A_YEAST 2-130  
Sc | Small ribosomal subunit protein uS12A | RS23A_YEAST 2-145  
Sd | Small ribosomal subunit protein eS24A | RS24A_YEAST 2-135  
Se | Small ribosomal subunit protein eS26A | RS26A_YEAST 2-95  
Sf | Small ribosomal subunit protein eS27A | RS27A_YEAST 2-82  
Sg | Small ribosomal subunit protein eS30A | RS30A_YEAST 2-61  
T | Large ribosomal subunit protein eL19A | RL19A_YEAST 2-189  
U | Large ribosomal subunit protein eL20A | RL20A_YEAST 2-172  
V | Large ribosomal subunit protein eL21A | RL21A_YEAST 2-160  
W | Large ribosomal subunit protein eL22A | RL22A_YEAST 9-108  
X | Large ribosomal subunit protein uL14A | RL23A_YEAST 2-137  
Y | Large ribosomal subunit protein eL24A | RL24A_YEAST 1-126  
Z | Large ribosomal subunit protein uL23 | RL25_YEAST 22-142  
a | Large ribosomal subunit protein uL24A | RL26A_YEAST 2-126  
b | Large ribosomal subunit protein eL27A | RL27A_YEAST 2-136  
c | Large ribosomal subunit protein uL15 | RL28_YEAST 2-149  
d | Large ribosomal subunit protein eL29 | RL29_YEAST 2-59  
e | Large ribosomal subunit protein eL30 | RL30_YEAST 9-104  
f | Large ribosomal subunit protein eL31A | RL31A_YEAST 4-112  
g | Large ribosomal subunit protein eL32 | RL32_YEAST 2-128  
h | Large ribosomal subunit protein eL33A | RL33A_YEAST 2-107  
i | Large ribosomal subunit protein eL34A | RL34A_YEAST 2-113  
j | Large ribosomal subunit protein uL29A | RL35A_YEAST 2-120  
k | Large ribosomal subunit protein eL36A | RL36A_YEAST 2-100  
l | Large ribosomal subunit protein eL37A | RL37A_YEAST 2-82  
m | Large ribosomal subunit protein eL38 | RL38_YEAST 2-78  
n | Large ribosomal subunit protein eL39 | RL39_YEAST 2-51  
o | Large ribosomal subunit protein eL40A | RL40A_YEAST 77-128  
p | Large ribosomal subunit protein eL41A | RL41A_YEAST 1-25  
q | Large ribosomal subunit protein eL42A | RL44A_YEAST 2-104  
r | Large ribosomal subunit protein eL43A | RL43A_YEAST 2-92  
s t | tRNA |   
x | Elongation factor 2 | EF2_YEAST 1-842  
  
1555 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select #24/Sa:2@CB

1 atom, 1 residue, 1 model selected  

> view matrix models #24,1,0,0,-69.815,0,1,0,11.635,0,0,1,170.62

> view matrix models
> #24,0.78973,0.5874,-0.17687,-136.41,-0.22404,0.0077634,-0.97455,635.95,-0.57108,0.80926,0.13773,327.52

> view matrix models
> #24,0.95608,0.25594,-0.14284,-95.118,-0.16787,0.078686,-0.98266,600.48,-0.24026,0.96349,0.11819,189.78

> view matrix models
> #24,0.95608,0.25594,-0.14284,-126.93,-0.16787,0.078686,-0.98266,643,-0.24026,0.96349,0.11819,89.833

> view matrix models
> #24,0.95608,0.25594,-0.14284,-91.844,-0.16787,0.078686,-0.98266,525.26,-0.24026,0.96349,0.11819,31.119

> view matrix models
> #24,0.95608,0.25594,-0.14284,-53.887,-0.16787,0.078686,-0.98266,553.2,-0.24026,0.96349,0.11819,4.3094

> view matrix models
> #24,0.98965,0.088516,0.11298,-82.393,0.1004,0.1355,-0.98568,458.46,-0.10256,0.98682,0.12521,-44.873

> view matrix models
> #24,0.98965,0.088516,0.11298,-83.915,0.1004,0.1355,-0.98568,454.09,-0.10256,0.98682,0.12521,-38.336

> rename #60 id #54

> rename #24 id #55

> rename #55 "compact eEF2"

> hide #!8 models

> select #55/x:596@O

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

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

> select up

6559 atoms, 6685 bonds, 842 residues, 1 model selected  

> show sel cartoons

> select up

209284 atoms, 224610 bonds, 17371 residues, 1 model selected  

> hide sel atoms

> select clear

> show #!61 models

> select #61/eEF2:367

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

> color sel #008f00ff

> color sel #4f8f00ff

> select clear

> select #55/x:641

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

> select up

31 atoms, 31 bonds, 5 residues, 1 model selected  

> select up

6559 atoms, 6685 bonds, 842 residues, 1 model selected  

> color sel #8efa00ff

> color sel #4f8f00ff

> select clear

> hide #!61 models

> hide #!55 models

> show #!8 models

> show #!55 models

> hide #!8 models

> show #!58 models

Drag select of 17924 residues, 11 pseudobonds  

> select subtract #58/ET

214051 atoms, 11 pseudobonds, 17847 residues, 3 models selected  

> show #!52 models

> hide #!52 models

> show #!53 models

> hide #!55 models

> hide #!58 models

Drag select of 440 residues  

> show #!55 models

> show #!58 models

> hide #!53 models

> hide #!55 models

> hide #!58 models

> show #!8 models

> color zone #8 near sel distance 60

> show #!55 models

> show #!59 models

> hide #!55 models

> show #!55 models

> hide #!59 models

> volume splitbyzone #8

Opened UnPre_cEF2_filtsharp.mrc 0 as #24.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 1 as #24.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 2 as #24.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 3 as #24.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 4 as #24.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 5 as #24.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 6 as #24.7, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  

> close #24

> hide #!55 models

> show #!58 models

> show #!55 models

> show #!61 models

> hide #!61 models

> show #!61 models

> hide #!55 models

> hide #!58 models

Drag select of 4227 residues, 9 pseudobonds  
Drag select of 6834 residues, 9 pseudobonds  

> select (sel & #61/18S)

27995 atoms, 31300 bonds, 1054 pseudobonds, 1313 residues, 3 models selected  

> hide #!61 models

> show #!58 models

Drag select of 17082 residues, 11 pseudobonds  

> select subtract #58/ET

235487 atoms, 31300 bonds, 1065 pseudobonds, 18318 residues, 5 models selected  

> hide #!58 models

> show #!55 models

> show #!52 models

> hide #!52 models

> show #!53 models

Drag select of 1282 residues  

> show #!8 models

> color zone #8 near sel distance 60

> hide #!55 models

> hide #!53 models

> show #!61 models

> hide #!8 models

> show #!55 models

> show #!8 models

> show #!59 models

> hide #!8 models

> hide #!55 models

> hide #!59 models

> hide #!61 models

> show #!61 models

> hide #!61 models

> show #!61 models

Drag select of 1927 residues, 2 pseudobonds  

> select subtract #61/eEF2

21613 atoms, 2 pseudobonds, 1870 residues, 2 models selected  

> show #!58 models

> hide #!61 models

Drag select of 17082 residues, 11 pseudobonds  

> select subtract #58/ET

229105 atoms, 13 pseudobonds, 18875 residues, 4 models selected  

> hide #!58 models

> show #!55 models

> show #!52 models

> hide #!52 models

> show #!53 models

Drag select of 1282 residues  

> hide #!53 models

> hide #!55 models

> show #!8 models

> color zone #8 near sel distance 60

> show #!55 models

> show #!58 models

> hide #!8 models

> show #!59 models

> show #!61 models

> hide #!55 models

> hide #!58 models

> hide #!59 models

> show #!59 models

> hide #!61 models

> show #!58 models

> hide #!58 models

> hide #!59 models

> show #!61 models

> show #!8 models

> show #!55 models

> volume splitbyzone #8

Opened UnPre_cEF2_filtsharp.mrc 0 as #24.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 1 as #24.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 2 as #24.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 3 as #24.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 4 as #24.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 5 as #24.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  
Opened UnPre_cEF2_filtsharp.mrc 6 as #24.7, grid size 270,270,270, pixel 2.59,
shown at level 0.00661, step 1, values float32  

> name frozen unpre2colourdivisions sel

> select add #55

442193 atoms, 224610 bonds, 4878 pseudobonds, 36686 residues, 8 models
selected  

> select subtract #55

232909 atoms, 13 pseudobonds, 19315 residues, 5 models selected  

> select add #61

418362 atoms, 221714 bonds, 5080 pseudobonds, 35048 residues, 7 models
selected  

> select subtract #61

211296 atoms, 11 pseudobonds, 17445 residues, 3 models selected  

> hide #!61 models

> hide #!55 models

> hide #!24.1 models

> color #24.2 #d6d6d61a models

> color #24.3 #a9a9a942 models

> color #24.3 #a9a9a941 models

> hide #!24 models

> show #!9 models

> show #!58 models

> color zone #9 near sel distance 60

> volume splitbyzone #9

Opened UnPre_none_filtsharp.mrc 0 as #25.1, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 1 as #25.2, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 2 as #25.3, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 3 as #25.4, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 4 as #25.5, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  
Opened UnPre_none_filtsharp.mrc 5 as #25.6, grid size 270,270,270, pixel 2.59,
shown at level 0.00679, step 1, values float32  

> hide #!25.1 models

> color #25.2 #d6d6d61a models

> color #25.3 #a9a9a945 models

> color #25.3 #a9a9a941 models

> color #25.3 #a9a9a948 models

> hide #!58 models

> save
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/20260217_FinaldensitiesWIP.cxs
> includeMaps true

> show #!24 models

> show #!23 models

> show #!22 models

> show #!21 models

> show #!20 models

> show #!19 models

> show #!18 models

> surface dust #18-26 size 10

> surface dust #18-26 size 20

> surface dust #18-26 size 40

> surface dust #18-26 size 30

> surface dust #18-26 size 20

> surface undust all

> hide #!19 models

> hide #!20 models

> hide #!21 models

> hide #!22 models

> hide #!23 models

> hide #!24 models

> hide #!25 models

> surface dust #18-26 size 7

> surface dust #18-26 size 2

> surface dust #18-26 size 5

> surface dust #18-26 size 8

> surface dust #18-26 size 7

> surface dust #18-26 size 5

> surface undust #18-26 size 5

Expected fewer arguments  

> surface undust #18-26

> surface undust #18.2,18.3 size 25

Expected fewer arguments  

> surface dust #18.2,18.3 size 25

No surfaces specified  

> surface dust #18.2 size 25

> surface dust #18.3 size 25

> surface dust #18.4 size 3

> surface dust #18.5 size 3

> surface dust #18 size 5

> surface dust #18 size 1

> surface dust #18 size 5

> surface dust #18 size 8

> surface dust #18 size 10

> surface dust #18 size 5

> surface dust #18 size 20

> surface dust #18 size 1

> surface dust #18 size 20

> surface dust #18.7 size 3

> surface dust #18.7 size 5

> surface dust #18.7 size 3

> surface dust #18.7 size 5

> surface dust #18.7 size 10

> surface dust #18.7 size 15

> surface dust #18 size 20

> surface dust #18.7 size 15

> surface dust #18 size 15

> hide #!18 models

> show #!19 models

> surface dust #19 size 15

> surface dust #19 size 20

> hide #!19 models

> show #!20 models

> surface dust #20 size 15

> surface dust #20 size 5

> surface dust #20 size 7

> surface dust #20 size 0

> surface dust #20 size 7

> surface dust #20 size 20

> surface dust #20.6 size 5

> surface dust #20.6 size 6

> surface dust #20.6 size 7

> surface dust #20.5 size 7

> surface dust #20.5 size 10

> surface dust #20.5 size 7

> hide #!20 models

> show #!21 models

> surface dust #21 size 20

> surface dust #21 size 30

> hide #!21 models

> show #!20 models

> hide #!20 models

> show #!22 models

> surface dust #22 size 30

> show #!14 models

> hide #!22 models

> show #!22 models

> hide #!14 models

> show #!14 models

> hide #!22 models

> show #!22 models

> hide #!22 models

> show #!22 models

> show #!13 models

> hide #!13 models

> hide #!14 models

> open
> /Users/campbell/Desktop/workspaces/hd_tn298-Comb_2025/BfactorScreener/20260216_MMS_Rotated_Bfactorscreening/LocRes_Bfac_-300_locres_filtered.mrc

Opened LocRes_Bfac_-300_locres_filtered.mrc as #26, grid size 270,270,270,
pixel 2.59, shown at level 0.0132, step 2, values float32  

> select #26

2 models selected  

> view matrix models #26,1,0,0,85.451,0,1,0,93.55,0,0,1,25.559

> hide #!26 models

> show #!14 models

> hide #!22 models

> show #!26 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!26 models

> hide #!22.5 models

> show #!22.5 models

> hide #!22 models

> hide #!6 models

> show #!22 models

> hide #!14 models

> hide #!22 models

> show #!6 models

> show #!22 models

> hide #!6 models

> show #!14 models

> hide #!22 models

> show #!22 models

> hide #!14 models

> show #!14 models

> hide #!22 models

> show #!22 models

> hide #!14 models

> show #!14 models

> show #!21 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!26 models

> hide #!26 models

> hide #!22 models

> show #!21 models

> hide #!21 models

> show #!22 models

> hide #!14 models

> hide #!22 models

> show #!21 models

> hide #!21 models

> show #!22 models

> hide #!22 models

> show #!21 models

> show #!14 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> hide #!14 models

> show #!14 models

> show #!22 models

> hide #!14 models

> show #!14 models

> hide #!22 models

> color #22.5 #fea33eff models

> show #!22 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> surface dust #22 size 15

> surface undust #22

> hide #!22 models

> show #!14 models

> hide #!14 models

> show #!15 models

> hide #!15 models

> show #!23 models

> surface dust #23 size 20

> surface dust #23 size 30

> surface dust #23 size 40

> hide #!23 models

> show #!24 models

> select subtract #26

Nothing selected  

> surface dust #24 size 20

> surface dust #24 size 5

> surface dust #24 size 20

> hide #!24 models

> show #!25 models

> surface dust #25 size 20

> surface dust #25 size 25

> surface dust #25 size 15

> show #!24 models

> hide #!24 models

> surface dust #25 size 5

> surface dust #25 size 15

> surface dust #25 size 20

[Repeated 1 time(s)]

> show #!24 models

> hide #!25 models

> hide #!24 models

> show #!25 models

> hide #!25 models

> show #!24 models

> hide #!24 models

> show #!25 models

> show #!24 models

> hide #!24 models

> hide #!25 models

> show #!24 models

> hide #!24 models

> show #!23 models

> hide #!23 models

> show #!22 models

> hide #!22 models

> show #!21 models

> show #!22 models

> hide #!21 models

> lighting full

> show #!25 models

> hide #!22 models

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting simple

> hide #!25 models

> show #!24 models

> hide #!24 models

> show #!25 models

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes true width 2

> graphics silhouettes true width 1

> graphics silhouettes true width 3

> graphics silhouettes true width 2

> graphics silhouettes true

> graphics silhouettes true depthJump 0.01

> graphics silhouettes true depthJump 0.02

> graphics silhouettes true depthJump 0.01

> graphics silhouettes true depthJump 0.03

> graphics silhouettes true depthJump 0.02

> hide #!25 models

> show #!24 models

> hide #!24 models

> show #!23 models

> graphics silhouettes true depthJump 0.01 width 1

> show #!24 models

> hide #!23 models

> hide #!24 models

> show #!25 models

> hide #!25 models

> show #!24 models

> hide #!24 models

> show #!23 models

> hide #!23 models

> show #!22 models

> hide #!22 models

> show #!21 models

> hide #!21 models

> show #!20 models

> hide #!20 models

> show #!19 models

> hide #!19 models

> show #!18 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!18 models

> show #!18 models

> hide #!10 models

> show #!10 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> lighting simple

[Repeated 1 time(s)]

> lighting full

> lighting simple

> lighting full

> graphics silhouettes true depthJump 0.01 width 1

> lighting full

> graphics silhouettes true width 2

> show #!18 models

> hide #!10 models

> show #!10 models

> hide #!18 models

> lighting full

[Repeated 1 time(s)]

> graphics silhouettes true depthJump 0.01 width 1

> graphics silhouettes true depthJump 0.01 width 1 width 1.5

Repeated keyword argument "width"  

> graphics silhouettes true depthJump 0.01 width 1.5

> hide #!10 models

> show #!18 models

> hide #!18 models

> show #!19 models

> hide #!19 models

> show #!20 models

> hide #!20 models

> show #!21 models

> hide #!21 models

> show #!22 models

> hide #!22 models

> show #!23 models

> hide #!23 models

> show #!19 models

> show #!11 models

> hide #!11 models

> color #19.4 #71a507ff models

> show #!11 models

> hide #!19 models

> show #!19 models

> color #19.4 #669900ff models

> hide #!11 models

> show #!11 models

> hide #!11 models

> color #19.4 #71a507ff models

> color #19.4 #669900ff models

> hide #!19 models

> show #!20 models

> color #20.4 #669900ff models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> hide #!20 models

> show #!21 models

> show #!13 models

> hide #!13 models

> hide #!21 models

> show #!22 models

> color #22.5 #ff9933ff models

> surface dust #22 size 5

> surface dust #22 size 10

> hide #!22 models

> show #!23 models

> color #23.6 #fea33eff models

> color #23.6 #ff9933ff models

> color #23.5 #669900ff models

> hide #!23 models

> show #!24 models

> color #24.7 #669900ff models

> hide #!24 models

> show #!25 models

> hide #!25 models

> show #!12 models

> lighting soft

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting full

> graphics silhouettes true depthJump 0.01 width 1.5

> undo

> show #!15 models

> hide #!15 models

> show #!16 models

> hide #!16 models

> show #!12 models

> hide #!12 models

> show #!18 models

> show #!19 models

> show #!20 models

> show #!21 models

> show #!22 models

> show #!23 models

> show #!24 models

> show #!25 models

> save
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/20260217_FinaldensitiesWIP.cxs
> includeMaps true

——— End of log from Tue Feb 17 16:29:23 2026 ———

> view name session-start

opened ChimeraX session  

> close #26

> rename #18 id #26

> rename #10 id #18

> save
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/20260217_FinaldensitiesWIP.cxs
> includeMaps true

——— End of log from Fri Feb 20 10:54:41 2026 ———

> view name session-start

opened ChimeraX session  

> open
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/MMS_Outputs/Rotated_filt.mrc

Opened Rotated_filt.mrc as #10, grid size 270,270,270, pixel 2.59, shown at
level 0.00669, step 2, values float32  

> select #10

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #10,1,0,0,-102.02,0,1,0,-88.765,0,0,1,-91.88

> view matrix models #10,1,0,0,-96.025,0,1,0,-89.937,0,0,1,-96.764

> fitmap #10 inMap #50

Fit map Rotated_filt.mrc in map Stable_60S.mrc using 24595 points  
correlation = 0.785, correlation about mean = 0.2895, overlap = 130  
steps = 64, shift = 3.67, angle = 0.374 degrees  
  
Position of Rotated_filt.mrc (#10) relative to Stable_60S.mrc (#50)
coordinates:  
Matrix rotation and translation  
0.99999181 -0.00087078 -0.00395356 -93.41351100  
0.00085056 0.99998657 -0.00511144 -90.54711300  
0.00395796 0.00510804 0.99997912 -96.93911107  
Axis 0.78381459 -0.60679855 0.13202353  
Axis point 0.00000000 18086.94381938 -21450.90984344  
Rotation angle (degrees) 0.37351787  
Shift along axis -31.07325861  
  

> hide #!19 models

> hide #!20 models

> hide #!21 models

> hide #!22 models

> hide #!23 models

> hide #!24 models

> hide #!25 models

> hide #!26 models

> volume #10 step 1

> select clear

> show #!51 models

> show #!59 models

> hide #!10 models

Drag select of 17213 residues, 12 pseudobonds  

> ui tool show "Color Zone"

> color zone #10 near sel distance 15.54

> color zone #10 near sel distance 6

> color zone #10 near sel distance 60

> show #!10 models

> hide #!51 models

> hide #!59 models

> select clear

> volume splitbyzone #10

Opened Rotated_filt.mrc 0 as #27.1, grid size 270,270,270, pixel 2.59, shown
at level 0.00669, step 1, values float32  
Opened Rotated_filt.mrc 1 as #27.2, grid size 270,270,270, pixel 2.59, shown
at level 0.00669, step 1, values float32  
Opened Rotated_filt.mrc 2 as #27.3, grid size 270,270,270, pixel 2.59, shown
at level 0.00669, step 1, values float32  
Opened Rotated_filt.mrc 3 as #27.4, grid size 270,270,270, pixel 2.59, shown
at level 0.00669, step 1, values float32  
Opened Rotated_filt.mrc 4 as #27.5, grid size 270,270,270, pixel 2.59, shown
at level 0.00669, step 1, values float32  

> save
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/rotationWIP.cxs
> includeMaps true

——— End of log from Fri Feb 20 14:46:45 2026 ———

> view name session-start

opened ChimeraX session  

> color #27.2 #d6d6d619 models

> color #27.3 #a9a9a942 models

> color #27.3 #a9a9a93f models

> color #27.5 #ff9933ff models

> hide #!27.1 models

> surface dust #27.2 size 25.9

> surface dust #27.3 size 25.9

> surface dust #27.4 size 25.9

> surface dust #27.5 size 25.9

> show #!23 models

> hide #!27 models

> show #!27 models

> hide #!23 models

> show #!21 models

> lighting full

> hide #!21 models

> show #!21 models

> hide #!27 models

> lighting full

> lighting simple

> lighting full

> lighting flat

> lighting full

> graphics silhouettes true jumpDepth 0.01

Expected a keyword  

> graphics silhouettes true depthJump 0.01

> graphics silhouettes true width 1.5 depthJump 0.01

> graphics silhouettes true width 2 depthJump 0.01

> graphics silhouettes true width 2 depthJump 0.02

> graphics silhouettes true width 2 depthJump 0.03

> graphics silhouettes true width 2 depthJump 0.01

> graphics silhouettes true width 2 depthJump 0.015

> show #!27 models

> hide #!21 models

> show #!23 models

> hide #!27 models

> show #!27 models

> hide #!23 models

> save /Users/campbell/Desktop/image1.png supersample 3

> save
> /Users/campbell/Desktop/Chimera_sessions/Manuscript1/Ribofigs/20260217_FinaldensitiesWIP.cxs
> includeMaps true

——— End of log from Fri Feb 20 15:29:20 2026 ———

> view name session-start

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,3
      Model Number: Z1C9000SED/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 Performance and 4 Efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.81.10
      OS Loader Version: 13822.81.10

Software:

    System Software Overview:

      System Version: macOS 26.3 (25D125)
      Kernel Version: Darwin 25.3.0
      Time since boot: 1 day, 2 hours, 17 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        HP U32 4K HDR:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Television: Yes


Installed Packages:
    alabaster: 1.0.0
    annotated-types: 0.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.6.0
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    geomdl: 5.4.0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    pandas: 2.3.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pyarrow: 21.0.0
    pycollada: 0.8
    pydantic: 2.11.7
    pydantic_core: 2.33.2
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    starfile: 0.5.13
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing-inspection: 0.4.1
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

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#19908 new defect

ChimeraX bug report submission

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