VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Aug 26 2010 - 10:12:42 CDT

Hi,

You could use
animate write pdb $i.pdb
to write the frames to pdbs (add an aditional counter so that your frames
would be numbered 1.pdb 2.pdb etc...) and than use the
animatepdbs<http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/>script
to load the files in a new trajectory.

Or perhaps you could just delete the frames you don't need from the
trajectory using animate
delete<http://www.ks.uiuc.edu/Research/vmd/current/ug/node117.html>
and
then save this as a new trajectory using animate write dcd traj.dcd or
something similar.

Regards,
Ajasja

On Thu, Aug 26, 2010 at 16:01, Pat Yee <pyee_at_nd.edu> wrote:

> Hi VMD users,
>
>
>
> Im trying to make a DCD file containing select frames of another DCD file.
> The frames I want in the new DCD file will be taken when two atoms (in this
> case atom1 and atom2) are between 3.23 and 3.43 angstroms apart. So far Ive
> only made a script that makes a file containing the frames where this
> happens. For example, my output might say:
>
>
>
> 123
>
> 456
>
> 789
>
>
>
> I want to make a DCD file with only frames 123, 456, and 789.
>
>
>
> Can anybody tell me how to modify my script to get what I want? I attached
> the script and a sample output to this email.
>
>
>
> *Pat Yee*
>
>
>