VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 31 2005 - 17:29:09 CST

Hi,
  You can use the "color by volume" method to color by the density, but
an isosurface is by definition a surface that follows a single density value
through space, so it would usually be colored a solid color. In areas where
there's an extremely strong density gradient, you can color by volume and
alter the min/max color scale values (in the trajectory tab) and get VMD
to show you the nearby gradient if you make the min/max values sufficiently
close to the isovalue for the surface you're rendering, but in general it
makes more sense to color another surface by this density and not an
isosurface itself, as you won't be able to show anything but very strong
density gradients.

  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Oct 29, 2005 at 07:42:13PM +0800, Yang Zhenyu wrote:
> Dear VMD users
>
> I proceed Graphic>>Representations>>Draw style>>Drawing Method>>isosurface to plot result of CPMD result. But I can't find way to change the colour of the isosurface(I want to make the colours to show the difference of the density), and I want to ask what does "isovalue" mean here.
>
> Any suggestions will be appreciated!
>
>
>
>
> 　　　　　　　
> 　Best Regards
>
> 　Yang Zhenyu
> State Key Laboratory of Nonlinear Mechanics (LNM)
> Institute of Mechanics, Chinese Academy of Sciences
> No.15 Beisihuanxi Road
> Beijing 100080, P. R. China
> FAX: 010-62579511
> 　yangzy_at_lnm.imech.ac.cn
> 　2005-10-29
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078