From: Patrick Redmill (patrickredmill_at_gmail.com)
Date: Mon Oct 05 2009 - 05:41:39 CDT

Axel/Schreiner,
Thanks a lot! Like Axel mentioned, the writepdb line was a little
problematic, but changing

> $a writepdb frame-$a.pdb

to $a writepdb $fr.pdb gave seems to give the desired result. Nevertheless,
the initial post got me close enough to get this fixed before bedtime :).
Thanks again for the quick responses! I will keep storage issues with .pdbs
in mind, thusfar neither the size of the files or the loss in precision
hasn't bit me yet.

Patrick

On Mon, Oct 5, 2009 at 1:41 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Sun, 2009-10-04 at 22:06 -0500, Schreiner Eduard wrote:
> > Hi Patrick,
> >
> > something like the following should work (I did not test it)
> >
> > mol new yourtraj.xyz waitfor all
> > set nr_frames [molinfo 0 get numframes ]
> > set a [atomselect top "all" frame 0]
> >
> > for {set fr 0} {$fr < $nr_frames} {incr fr } {
> > $a frame $fr
> > $a update
>
> $a update is not needed for an "all" selection.
> the number of atoms in the selection will not change.
>
> > $a writepdb frame-$a.pdb
>
> this cannot work ($a is the selection and $fr the loop variable)
> to get _exactly_ what was asked for try:
> $a writepdb [format "frame-%03d.pdb" $fr]
>
> > }
> > $a delete
> >
> >
> > keep in mind, the size (storage space) requirements will increase
> > if you go from xyz to pdb format.
>
> not that much. the .pdb format drops a lot
> of precision on the coordinates. this is different
> if you start from a binary format.
>
> cheers,
> axel.
>
> >
> >
> > eddi
> >
> >
> > On Oct 4, 2009, at 9:48 PM, Patrick Redmill wrote:
> >
> > > Hi all,
> > > I think this is an easy question, hope I'm right. I have an xyz
> > > trajectory, and I wish to loop through each frame and save each
> > > frame as an individual .pdb file (numbered 000.pdb, 001.pdb,
> > > 002.pdb, ... etc.). I don't need any of the extra connectivity data
> > > that comes with the pdb, just the format change. This is easily done
> > > in the GUI with File > Save coordinates, but given that I may be
> > > dealing with a few hundred frames, I'd like to automate it if
> > > possible. Thanks in advance!
> > >
> > > Patrick
> > >
> > >
> >
> >
> > =====================================================
> > Eduard Schreiner
> > Theoretical and Computational Biophysics Group
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
> > Phone: 217-244-4361
> > Fax: 217-244-6078
> > http://www.ks.uiuc.edu/~eschrein/ <http://www.ks.uiuc.edu/%7Eeschrein/>
> > =============================================
> >
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
>