VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Mon Jun 02 2008 - 11:51:09 CDT

On Mon, Jun 02, 2008 at 11:15:58AM -0500, Leonardo Trabuco wrote:
> On Mon, Jun 02, 2008 at 04:01:49PM +0000, Claw Isthelaw wrote:
> >
> > Dear VMD Community,
> >
> > Given a list of integers (residue numbers) like:
> > {1153 1134 1128 1194 1123}, how can I create an atomselection containing all of those residues. I'm trying to write out a PDB file containing the entire protein and a list of water residues. I've tried the following:
> >
> >
> > ----------------------------------------------------------
> > set watlist1 {1153 1134 1128 1194 1123}
> >
> > foreach resid $watlist1 {
> > lappend watlist2 "resid $resid"
> > }
> >
> > set watlist3 [join $watlist2 " or "]
> >
> > animate write pdb new.pdb sel [atomselect top "protein or [puts $watlist3]"]
> > ---------------------------------------------------------
> >
> >
> > I have tried some other things too. Is there an easier way to be doing this?
>
> Yes.
>
> set sel [atomselect top {protein or (water and resid 1153 1134 1128 1194 1123}]

I had a typo. This should read:
set sel [atomselect top {protein or (water and resid 1153 1134 1128 1194 1123)}]

Leo

> $sel writepdb new.pdb
>
> Best,
> Leo
>
> > Thanks,
> > Jeff Tibbitt
> >
> > _________________________________________________________________
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> >
>
> --
> Leonardo Trabuco, Ph.D. student
> Theoretical and Computational Biophysics Group
> University of Illinois at Urbana-Champaign
> 

-- 
Leonardo Trabuco, Ph.D. student
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign