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
