From: Martin, Erik W (
Date: Mon Feb 23 2015 - 17:38:36 CST

I suppose you could just go into the pdb file as text and and just delete the sidechain atoms manually. If you are concerned with numbering, you could open that pdb file then rewrite it in vmd.

However, slightly more elegantly, you could make these commands in the tk console of vmd

% set protein [atomselect top "all and not {sidechain and resid X}]

% $protein writepdb filename.pdb

..where X is the resid of of the residue you want to remove the sidechain from and filename is your new pdb.

Hope this helps,


From: <> on behalf of Ashar Malik <>
Sent: Monday, February 23, 2015 3:57 PM
To: Jevgenij Raskatov
Subject: Re: vmd-l:

Hi there,

Not sure how that would be done through vmd. However what you can do is write the the complete PDB file of the structure. Then use a simple script (python/shell) to parse the PDB file and copy the backbone atoms of the residue of interest and all atoms from other residues.

Hope this helps.


On Feb 24, 2015 5:49 AM, "Jevgenij Raskatov" <<>> wrote:
Dear all,

I would like to write a pdb file, in which one amino acid is selected as backbone only, whereas the rest contains all atoms - how does one combine that?


Dr. Jevgenij A. Raskatov
Assistant Professor in Chemistry and Biochemistry
Tel.: +1-831-459-2978<tel:%2B1-831-459-2978>
Department of Chemistry and Biochemistry
Physical Science Building 356
1156 High Street
Santa Cruz, CA
95064 USA