Hi Elaine, Thanks for the help. This will speed things up quite a bit. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 ________________________________________ From: chimera-users-request@cgl.ucsf.edu <chimera-users-request@cgl.ucsf.edu> Sent: Tuesday, August 1, 2023 3:00 PM To: chimera-users@cgl.ucsf.edu Subject: [EXTERNAL] Chimera-users Digest, Vol 243, Issue 22 Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Measure rotation without writing PDB (Reza Khayat) 2. Re: Measure rotation without writing PDB (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Tue, 1 Aug 2023 18:23:19 +0000 From: Reza Khayat <rkhayat@ccny.cuny.edu> Subject: [Chimera-users] Measure rotation without writing PDB To: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Message-ID: <1690914198332.72284@ccny.cuny.edu> Content-Type: multipart/alternative; boundary="_000_169091419833272284ccnycunyedu_" 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