From: Ashar Malik (
Date: Tue Jan 16 2018 - 01:52:23 CST

Create two representations. One of cartoon type and the other of line type.
The cartoon type will have the word *protein *in selection.
The line type will have the word *protein and not hydrogens*

Are you interested in removing the carboxyl and amino groups from terminal
residues only ? or from charged residues as well?
You can add atom names to the line type selection above and the line will
be drawn for only those atoms that you allow.

All of this can be done in graphical mode by selecting
and then making selections and creating representations for those
The same can be done from command line as well. But as that needs more
details I will get into that if you need it.

Hope this helps.

On Tue, Jan 16, 2018 at 5:51 PM, Roshan Shrestha <>

> Dear all,
> In my simulation, I want to see which and how sidechains are
> interacting, so Is there any way I can represent the sidechains in VMD so
> that it sticks out of New cartoon representation of protein, with no
> hydrogen, carboxyl and amino groups.
> Thanks
> --
> Roshan Shrestha
> M.Sc (Physics)
> Central Department of Physics, Tribhuvan University
> Kathmandu, Nepal