VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 24 2018 - 10:02:58 CDT

Hi,
  It is also worth noting that "residue" is the residue numbering assigned
internally by VMD, which is unrelated to whatever was provided by your
input files. It is a zero-based unique residue numbering unlike what
you may have expected from a PDB, for example. See the User's Guide
for more information about the different residue fields.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 24, 2018 at 07:47:57AM -0400, Giacomo Fiorin wrote:
> In general, VMD supports several Tcl commands to operate on vectors, and
> the following plugin:
> https://github.com/jhenin/vecexpr
> enables many more options.
>
> Giacomo
>
> On Sat, Sep 22, 2018 at 9:42 AM subramanian vidhyasankar <svsquery_at_gmail.com>
> wrote:
>
> > Dear vmd users i tried to renumber the residues in psf file using the
> > following script
> >
> > set sel [atomselect top all]
> > $sel set resid [$sel get residue]
> > $sel writepdb renumbered.psf
> >
> > but the number starts from zero instead of one . Please give me
> > rectification of my script to give residues from number 1
> >
> >
> > with regards
> > S.vidhyasankar
> >
> >
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin 

-- 
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/