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 _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/