From: bo baker (bo.bybaker_at_gmail.com)
Date: Sat Feb 14 2009 - 17:16:27 CST

Hi, Peter:

The script works perfect now!

Thank you

Cheers

Bo

On 2/15/09, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> Hi Bo,
> it's because I messed up the syntax for measure bond (I said it was
> untested ;-)
> Try:
> foreach molid [molinfo list] {
> set sel1 [atomselect $molid "resid 621 and name C9A"]
> set sel2 [atomselect $molid "resid 900 and name C1A"]
>
> set ind1 [join [$sel1 get index]]
> set ind2 [join [$sel2 get index]]
> $sel1 delete
> $sel2 delete
>
>
> puts [measure bond [list [list $ind1 $molid] [list $ind2 $molid]]]
> }
>
> Sorry about that.
>
> Peter
>
> > Hi, Peter:
> >
> > I am quite confused. Not sure if something wrong with VMD itself.
> >
> > Here is how I did:
> >
> > ---load two pdb files (two conformations from protein docking)
> > ---use your script to plot the atoms distances, such as:
> > resid 621 and name C9A
> > resid 900 and name C1A
> >
> > Result is shown in "test-dist1.txt" file (attached)
> >
> > ----in VMD main window, creat graph presentatives from "selection"
> > using exact words above . Then measure bond distance between the two
> > atoms using "lable - bond".
> >
> > And the results are totally different.
> >
> > I have the two pdb files attached. I use VMD 1.8.6.
> >
> > Thank you for advice
> >
> > Bo
> >
> > On 2/14/09, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> >
> >> 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
> >> > > > >
> >> > > >
> >> > >
> >> >
> >>
> >>
>