From: Pawel Kedzierski (
Date: Tue Jan 16 2018 - 02:49:38 CST

W dniu 16.01.2018 o 05:51, Roshan Shrestha pisze:
> 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.
If you want to see both New Cartoon view of the backbone and the
sidechains as "sticks" (aka Bonds or Licorice), then you need two
graphical representations with different "Drawing Method" and selection
of atoms. A recommended reading is chapter "Selection methods
<>" of VMD
User Guide:
Basically, create another representation with "Create Rep" button.
Set "Drawing Method" of the first to New Cartoon.
Set "Drawing Method" of the second to (say) Licorice.
Change the Selection of the second representation to "name CA or sidechain".

You may also have a look at the documentation of Labels
<> which allow
you to e.g. plot a distance between selected atoms and more:
> Thanks
> --
> Roshan Shrestha
> M.Sc (Physics)
> Central Department of Physics, Tribhuvan University
> Kathmandu, Nepal
> /
> /