VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Wed Jul 22 2009 - 00:52:57 CDT

Dear Carmen,

On Tue, Jul 21, 2009 at 6:57 PM, Carmen
Valladares<cjvalladares_at_ucdavis.edu> wrote:
> Hi,
> The same thing is happpening to as it did for Vlad Cojocaru.  I am going
> through file------> save state
>
> I am doing a lot of protein comparisons and when I align two proteins I
> would like to save them as I left them.
> However every time I open the saved file again the graphical representation
> are saved but not any of the manipulations I did.
>
> Is there something I may be overlooking?

Yes. When you load a saved state, VMD will load the coordinates from
the files specified in the saved state. If you manipulate coordinates,
you want to save new coordinate files with the new coordinates. You
can do this through the GUI under File->Save Coordinates, or through
the console, e.g.:

set sel [atomselect top all]
$sel writepdb newfile.pdb
$sel delete

Cheers,
Leo

> --
> Carmen Valladares
> cjvalladares_at_ucdavis.edu
> ~~~~~~~~~~~~~~~~~~~~~~~~~~
> College of Engineering -
> Biological Systems Engineering
> ~~~~~~~~~~~~~~~~~~~~~~~~~~
> Mujeres Ayudando La Raza
> Co Coordinator 2008-2009
>
> 

-- 
Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign