From: John Stone (
Date: Wed Oct 29 2008 - 04:47:48 CDT

  I'm unable to follow your problem description to really understand
what it is that's giving you trouble. Perhaps the best thing would be
for you to create a snapshot image and send it so that we can actually
see what you're talking about. The resolution of the grid doesn't have a
direct relationship with the extent or contents of volume and resulting
displayed isosurface, so I'm not sure why you're listing those details.
The isosurfaces for two files with different sampling rates (resolution)
can vary considerably if you pick an inappropriate isovalue to display
(e.g. one that's in the "noise" for a particular volumetric dataset)
I would suggest rendering the isosurface with a solid surface rather
than points (to start with), and go from there.

  John Stone

On Tue, Oct 28, 2008 at 06:48:14PM +0100, Raluca Mihaela ANDREI wrote:
> Hi!
> I calculate the electrostatic potential of a protein with VMD
> and APBS. I get a .dx file that I import in VMD. Why I don't
> see dots in the whole volume of the box? I thought that the
> electrostatic potential is calculated in 129x129x129
> gridpositions counts. Then I calculated the electrostatic
> potential by APBS alone and I got a dx file with 97x65x65
> gridpositions counts. I represented these two files as
> isosurfaces (red for isovalue -1 and blue for isovalue 1). The
> isosurfaces of the two files are different. Can somebody tell
> me why?
> Thank you,
> Raluca

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