[Chimera-users] AFTER DOCKING I AM SAVING THE PDB FILES, BUT IN THAT PDB FILE THE LIGAND AND RECEPTOR ARE HAVING THE SAME NAME

[Elaine Meng]

Hi Shinjini,
It is unclear what name you are talking about.  There is a "model name", maybe the ligand and receptor are together in one model.  There is a "file name" of the saved PDB file.  There are "residue names," many different amino acids in the receptor, each one with its own name, and probably the ligand also has another different residue name.  Each atom also has an "atom name."

If you want separate files, just select the atoms you want in one file, use menu: File ... Save PDB and choose the option to "save selected atoms only".   Then select the atoms you want in the other file, and use the same process to save another PDB file.  You can name each file whatever you want.

Selecting atoms:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>

Saving PDB files:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

If you want to change residue names or atom names, maybe you just want to text-edit the PDB file directly (not using Chimera).  Here is some explanation of PDB file format so you can understand how to edit the text.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 7, 2020, at 7:37 AM, Shinjini Ghosh <shinjinighosh2014 at gmail.com> wrote:
> 
> For analysis, I want to have a PDB file of let's say with the first docked ligand in chimera which I did with autodock vina. I was able to save and open it in chimera. But the receptor and the ligand are both having the same name which I am using to save my PDB file. How can I change the names of receptor and ligand in the PDB file so that it is considered as different molecules in that particular PDB file. I want to give two different names to the receptor and the ligand in that particluar PDB file. This I need for my project.
> Please help me with this.
> Thank you.