VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 17 2005 - 18:45:02 CDT

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
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