From: bo baker (bo.bybaker_at_gmail.com)
Date: Thu Feb 12 2009 - 23:50:21 CST

---------- Forwarded message ----------
From: bo baker <bo.bybaker_at_gmail.com>
Date: Feb 13, 2009 4:48 PM
Subject: Re: vmd-l: Atom distances from trajotory
To: Peter Freddolino <petefred_at_ks.uiuc.edu>

Hi, Peter:

 I have a problem here with the script.

 The script itselfl works fine. I am able to get a set of data from all
 the pdb files loaded. But when I exam the data, there are big
 differences. I manullly measure ("label" ) the distance between the
 two atoms from the main VMD window from individaul pdb files, the
 value is much greater than those by the script. I wonder what could be
 wrong?

 Thank you for your advice

 Bo

On 2/13/09, bo baker <bo.bybaker_at_gmail.com> wrote:
> Thanks, Peter:
>
> Your script works perfect. And need "ind1" as well.
>
> Cheers
>
>
> Bo
>
>
> On 2/13/09, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> > You would need to do some scripting for this, something like (not tested)
> >
> > foreach molid [molinfo list] {
> > set sel1 [atomselect $molid "resid 615 and name OP1"]
> > set sel2 [atomselect $molid "resid 900 and name OG"]
> > set ind1 [join [$sel1 get index]]
> > set ind2 [join [$sel2 get index]]
> > $sel1 delete
> > $sel2 delete
> >
> > puts [measure bond [list $molid $ind1] [list $molid $ind2]]
> > }
> >
> > Note that if the indices of the two atoms you care about are the same in
> > all molecules, you don't need to use atoms selections to define ind1 and
> > ind2. If all of your molecules have the *same* number of atoms, then you
> > ought to load them all into one molecule as a trajectory instead, which
> > makes this much easier.
> >
> > Best,
> >
> > Peter
> >
> >
> >
> >
> > bo baker wrote:
> > > Hi, VMD:
> > >
> > > I have a set of pdb files and would like to plot the atomic distances
> > > from all of them. I ckecked "Lable" and "VolMap" tools. Both gives the
> > > distance from individue files but not of the all files.
> > >
> > > Can any one suggest if VMD could perform this task? For example, I
> > > would like to know the distance between 615 O1P and 900 OG through the
> > > entire pdb filed loaded.
> > >
> > > Thank you for your advice
> > >
> > > Bo
> > >
> >
>