VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 17 2013 - 09:50:33 CDT

Hi,
  Sorry for the slow reply.
There is a VMD plugin called "volutil" that you can use to perform various
manipulations on volumetric map data. To use it:
  package require volutil
  volutil (this will print the help message)

It is mainly used with DX files, but if I recall correctly it may also
read other formats supported by the VMD plugins.

You should be able to add maps together, average them, and various
other operations which should enable you to combine multiple occupancy
maps together. It should also handle cases where the maps do not precisely
overlap in space.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 17, 2013 at 09:31:04AM +0200, Axel Kohlmeyer wrote:
> On Mon, Jul 15, 2013 at 9:44 PM, Andrei Tudor <andrei.tudor.1_at_ulaval.ca> wrote:
> > Hello,
> >
> > I would like to know if it is possible to combine the occupancy maps obtained with volmap from multiple trajectories.
> > I have looked on the help page, but I didn't find any info regarding this.
>
> don't think so. a long time ago, i wrote a little tool that can
> combine multiple .cube files (which are used for density or potential
> maps in quantum chemistry). you should be able to save or convert the
> volume maps into cube format and use that tool. let me know and i'll
> dig it out and e-mail it to you
>
> since the .dx format usually written by VMD is fairly
> straightforward, it should also be possible to write such a tool
> yourself with whatever script language you are familiar with.
>
> axel.
>
> >
> > Thank you,
> > Andrei
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/