Hi Reza,

  Not sure you'll think this is simpler, but it avoids writing a temporary file.  You open two copies of the second pdb, align one copy using domain 1 and the other using domain 2 and then measure the rotation between the two copies

open pdb1
open pdb2
open pdb2
match #1:1-50 #0:1-50
match #2:55-80 #0:55-80
measure rotation #2 #1
close all

By the way, I suggest you use ChimeraX.   We have no funding for Chimera so you are more likely to get an answer to your question if it is about ChimeraX.  All the above steps work in ChimeraX.

  Tom


On Aug 1, 2023, at 11:23 AM, Reza Khayat via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi,

I'm trying to measure the movement of a domain between two structures of the same protein. Here are the conditions:
1. There are two domains in each structure
2. I want to overlay the first domain and measure the rotation of the second domain
3. There are lots of structures, so I want to minimise the number of steps
4. I'd like to do this with a script and the --no_gui option on headless Chimera

Here is my current script for the routine:
open pdb1
open pdb2
match #1:1-50 #0:1-50
write format pdb relative #1 #0 t.pdb
delete #1
open t.pdb
match #1:55-80 #0:55-80
measure rotation #1 #0
delete #1

open pdb3
...

Is it possible to not have to write, delete, and open #1 after the first match step? If I don't do this, then the measure rotation #1 #0 will measure rotation of the initial match rather than the second match. Thanks for the help. 

Best wishes,
Reza

Reza Khayat, PhD
Associate Professor 
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
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