VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 31 2017 - 17:18:19 CDT

Hi,
  In VMD, this is done using the Isosurface representation, and you
would need/want to set the isovalue to the correct value that extracts
the solvent accessible surface. As an alternative, you could ignore what
APBS computes there and compute the solvent surface using MSMS, Stride,
or NanoShaper, and color it using the electrostatic potentials (also
stored in a DX file) using the color by Volume method in VMD. Perhaps
read this little VMD minitutorial (10 years old, but it should still
work fine) as a starting point:
  http://www.ks.uiuc.edu/Research/vmd/minitutorials/colorbypot/

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Aug 11, 2017 at 05:19:24PM -0500, Rabeta Yeasmin wrote:
> Dear VMD Users,
>
> I have run a protein structure in APBS and got some output files ending
> with .dx, .cube. I want to get 3D figure of solvent accessible surface
> area of that protein. I have loaded the .dx file in pymol and vmd, but the
> figure was not clear. I am wondering if anyone can suggest me how can I
> get this.
> Thanks.
>
> Regards 

-- 
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/