VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 22 2020 - 12:43:25 CST

Hi,
  The VMD atom selection language has keywords "index" and "serial" for
0-based or 1-based atom selection by their sequential ordering. The selection
keywords for things like residues make use of information commonly found
in the PDB, so you have residue names or residue indices, fragment indices,
etc. I don't know the syntax of the selection language in MDAnalysis so
you'll have to answer that question for yourself, or ask other mailing
list contributors.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Jan 18, 2020 at 02:40:47PM +0545, Roshan Shrestha wrote:
> Hi everyone,
> My system consists of a dimer. So, VMD shows 2 proteins
> or 2 fragments. I am wondering if I can make selections for each peptide
> like by protein A or Fragment A. Also, is there any way we can also make a
> selection by atom number like that of *bynum 1:622* in MDAnalysis program.
> Thanks.
>
> With best regards
>
> --
> *Roshan Shrestha*
> M.Sc (Physics)
> Central Department of Physics, Tribhuvan University
> Kathmandu, Nepal 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/