VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Mar 08 2008 - 19:03:06 CST

Hi,
  Yes, the DX file is a Data Explorer (also OpenDX) file. You can
use the existing VMD DX plugin source code to read and process the
data if you like. Here's a very brief page describing the format
as used by VMD and other tools such as APBS:
  http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Mar 08, 2008 at 03:28:39PM -0800, Dong Xu wrote:
> > DX> Hi, I used VolMap plug-in and created an isosurface. I was wondering how to
> > DX> calculate the volume enclosed under the isosurface?
> >
> > since the grid generated by volmap is regular and there is
> > some smoothing involved, you could just dump the result in
> > a .dx file and write are small program/script that counts
> > the gridpoints with a value larger than your isovalue and
> > then multiplies with the size of the volume element.
> > i bet this already gives a pretty good approximation.
> > i've done this with cube files from electron structure
> > calculations and it worked amazingly well.
>
> Hi Alex, that's what I thought too. The problem is I'm not familiar
> with DX formatted file. Is it the same as openDX format? If you can
> point me to some reference about how the dx file is structured, I will
> probably be able to find or write a code to calculate the volume.
>
> Thanks!
>
> Dong Xu 

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NIH Resource for Macromolecular Modeling and Bioinformatics
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