[Chimera-users] Command line syntax questions

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 1 12:55:53 PDT 2018

Hi Divita,
You are welcome to try it, but I don’t think that approach will work.  That is, it will not let you combine without renumbering or changing chain ID when both input models already have the same residue number with same chain ID.  I believe I even tried that yesterday to confirm it didn’t work.
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 1, 2018, at 10:47 AM, Divita Mathur, Contractor Code 6910, FN <divita.mathur.ctr.in at nrl.navy.mil> wrote:
> Hi Elaine (and other Chimera users)
> I figured that if I have to text-edit eventually, I might as well text edit the molecule in the beginning (assign a random 'X' chainID), then before binding it to the DNA I changechains X A ('A' matches the chainID of the DNA); resrenumber 19 #1 (residue 19 is the desired residue number for the molecule after binding to DNA and #1 is the molecule model #) then I go ahead and combine. Here's the code:
> changechains #1:.X A; 
> resrenumber 19 #1; 
> sel #1 at P, #0.1:18 at O3’; 
> combine sel refSpec #0.1:18 newchainids false close true;
> This saves me the hassle of opening the pdb in text file to change the residue number of the molecule.

More information about the Chimera-users mailing list