VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 27 2011 - 14:47:03 CDT

Hi,
  The DX files are a visualization file format that can also be used to store
uniform grids of scalar data, which is what the 'volmap' commands do.
If you compute a density map from your structure, you'll get density values
of zero at the points associated with empty space, so that is a very simple
way to determine where you have pockets or cavities of empty space.
You could get a crude estimate of empty volume from this kind of approach,
but I should also point out that with a little google searching, that
I think that there are tools available that are specifically designed to
find cavity volumes. So, before you implement it yourself in a VMD
script, I would suggest googling for 15 or 20 minutes and see if you can
find one of those tools. I seem to remember I've heard of a couple such
programs in the past, but I don't remember them anymore.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 26, 2011 at 05:41:48PM +0000, BRAULIO FAVIÁN VALDEBENITO MATURANA wrote:
> Dear all,
>
> We're working on a Tcl/Tk script whose function is to determine both
> surface and internal cavities of a given protein. In order to achieve
> that, we've been thinking in the "volmap" function as stated by John Stone
> in reply to "cavity/pocket representation" on May 2nd, 2006 (it can be
> seen here:
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/6885.html), but
> instead of a graphical output, we need the analytical data too.
>
> Well, regarding the output of the "volmap" command, which is a file with
> .dx extension, we would like to know if there is any way to use the
> information on that file so that we can "substract" from the entire map
> the volume occupied by the actual molecule, thus letting the volume of any
> possible cavities.
>
> Thanks in advance!
> Braulio. 

-- 
NIH Resource 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/       Fax: 217-244-6078