[Chimera-users] Command line syntax questions

Divita Mathur, Contractor Code 6910, FN divita.mathur.ctr.in at nrl.navy.mil
Fri Jun 1 10:47:34 PDT 2018

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.

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 5/31/18, 3:43 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

    Hi Divita,
    I believe you just have to text-edit the PDB file to change the residue number if other atoms already have that same residue number.  As you said, “bond” only adds the bond without changing any numbering.
    Elaine C. Meng, Ph.D.
    UCSF Chimera(X) team
    Department of Pharmaceutical Chemistry
    University of California, San Francisco
    > On May 31, 2018, at 8:42 AM, Divita Mathur, Contractor Code 6910, FN <divita.mathur.ctr.in at nrl.navy.mil> wrote:
    > Hi Elaine
    > Thank you for your response. I am using the bond function to bind a molecule to DNA. But the bond function is not changing the residue number of the new molecule (which has a residue number 1), which is causing issues (as there is base #1 in the DNA). So far I am editing the pdb file as a text document like you said, but I was just wondering if there was another way.
    > Thank you, again! The Split function is working for me!

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