From: Axel Kohlmeyer (
Date: Mon Aug 07 2006 - 13:35:43 CDT

On Mon, 7 Aug 2006, Shirley Li wrote:

SL> Dear VMD expert,

hi shirley,

SL> I have some questions about VMD/APBS.

SL> For the .dx file generated from APBS, instead of showing the
SL> isosurface of each atom of the entire protein which makes the
SL> graphic too noisy, is there any selection tool in VMD which allows
SL> for the display of ONLY CENTAIN REGIONS, say within 6 angstroms of
SL> the ligand or the center?

last time i looked, no. but that should actually not be a big problem,
as people usually visualize electrostatic potential maps as color code
projected on a molecular surface. now you can easily create a molecular
surface of a selection using the MSMS or Surf representation and then
use the Volume colorization method to display the APBS map on the
generated surface. note that you have to adjust the Color Scale Range
to be symmetric around 0 if you want the 'middle color' (frequently
white or green) to represent a (close to) zero ES potential.

SL> Another question, what does the isovalue exactly mean? Say, one
SL> choose an isovalue of 1.0, does it allow to show grid points with
SL> value greater than, or less than, or equal to isovalue?

an isosurface is like an isoline in a 2-d map, it describes surface
through data points that have the same value.


SL> Thanks in advance.
SL> Shirley
SL> ---------------------------------
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Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.