VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Feb 13 2009 - 09:33:01 CST

Hi Bo,
are you sure that the atoms you've labeled have the same indices as the
ones being requested in the script? I'd suggest manually adding a Bonds
label, and then looking in the console to find the indices of those
atoms and verifying that you get the same answer using the measure bonds
command.

By the way, in your initial email it was ambiguous what you meant by
"615 O1P" and "900 OG". My script was written assuming the numbers are
residue IDs, but I don't know if that's what you meant.

Peter

bo baker wrote:
> ---------- 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
> > > >
> > >
> >
>