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