VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 17 2005 - 18:51:45 CDT

Hi,
  Oops, I wrote that a bit too fast and said it backwards:
The "residue" keyword is VMD's internal residue numbering,
'resid' comes from the PDB file. (smacks hand on forehead...)

  John

On Wed, Aug 17, 2005 at 06:45:02PM -0500, John Stone wrote:
>
> The problem here is that "residue 5" is not the same as "resid 5".
> "residue 5" is actually a GLY residue, not GLU. "resid 5" is a GLU...
> The "resid" keyword is VMD's internal residue numbering, not what's in the
> PDB.
>
> See for yourself:
> vmd > set sel [atomselect top "residue 5"]
> atomselect0
> vmd > $sel get residue
> 5 5 5 5 5
> vmd > $sel get resname
> GLY GLY GLY GLY GLY
> vmd > $sel get resid
> 6 6 6 6 6
> vmd > set sel [atomselect top "resid 5"]
> atomselect1
> vmd > $sel get residue
> 4 4 4 4 4 4 4 4 4 4
> vmd > $sel get resname
> GLU GLU GLU GLU GLU GLU GLU GLU GLU GLU
> vmd > $sel get resid
> 5 5 5 5 5 5 5 5 5 5
> vmd >
>
> John
>
>
>
> On Wed, Aug 17, 2005 at 07:25:35PM -0400, Mihaly Mezei wrote:
> > Hi,
> >
> > When I used
> >
> > residue 5
> >
> > it selected the backbone only.
> >
> > When I used
> >
> > resname GLU,
> >
> > it selected all atoms of all GLU.
> >
> > When I used
> >
> > resname GLU and residue 5
> >
> > it selected nothing.
> >
> > However, when I used
> >
> > resid 5
> >
> > it selected properly the whole residue.
> >
> > The same behavior was observed on the Windows wersio (Version 1.8.3, Feb.
> > 15, 2005) and the SGI version (version 1.8 (January 14, 2003).
> >
> > Thanks for the quick action.
> >
> > Best,
> > Mihaly
> >
> > Mezei, Dept. of Physiology & Biophysics, Mount Sinai School of Medicine
> > Voice: (212) 241-2186 Fax: (212) 860-3369|
> > WWW (MSSM home): http://directory.mssm.edu/faculty/mihaly.mezei
> > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
> >
>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078