[Chimera-users] Command line syntax questions

Divita Mathur, Contractor Code 6910, FN divita.mathur.ctr.in at nrl.navy.mil
Fri Jun 1 13:03:15 PDT 2018

Hi Elaine

I will give it a shot (with same residue number). Though I tried the code I sent in the last email and it worked - however, the residue number was different but chain IDs were the same. Now, the molecule is inserted between bases 18 and 20 as residue #19 (I ended up building the DNA with an unnecessary extra base which I deleted to make room for the molecule). Now, the two input models have same chain ID but different residue numbers. I can work with that! 

Like you said, perhaps identical residue numbers AND chain ID would not work.

Thank you for this discussion!

Divita Mathur
Postdoctoral Research Fellow

Center for Bio/Molecular Science and Engineering

Naval Research Laboratory

Washington DC 20375

(202) 767-0687 (Office)

divita.mathur.ctr.in at nrl.navy.mil
On 6/1/18, 3:56 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

    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.

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