VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Mon Feb 05 2007 - 09:11:38 CST

Dear Matt,
once you load the coordinates, create a selection for the molecules you
are interested in, ie
set PET [atomselect top " resname PET"]
then you can change their coordinates by using moveby
$PET moveby 0 0 1
and finally write the new coordinates, (only of your selected molecules)
$PET writepdb PETnewcoordinates.pdb

For more information about atom selection and coordinates manipulation
please check out the vmd documentation.
Regards
Cesar

wolfinbm_at_uci.edu escribió:
> Hello
> I am trying to save the positions of different PET molecules as I load
> them up and drag them around. If I attempt to save a structure something
> like this:
>
> (PET=Polyethylene Terephthalate molecule)
>
> PET PET PET PET
> PET PET PET PET
>
> as *.vmd
>
> I end up with garbage when I reload, i.e. 8 molecules with all their atoms
> in the same positions:
>
> PET <x8 in exact same position>
>
> I also can't find any other save function that doesn't involve saving just
> the information about a single molecule (it seems kind of ridiculous to
> have a coordinate file for what could be thousands of PET molecules in the
> membrane).
>
> Thanks for any help
> Matt Wolfinbarger
>
>
>