VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 16 2006 - 15:43:57 CDT

Ivan,
  At present the best choice of external renderer in terms of
emulating the "one-sided" transparent surface appearance one can
create using screen-door transparency in VMD may be Raster3D, which
has some unusual transparency rendering modes you can use.
Another way you can create the kind of figure you're looking for
is to render two images with VMD and combine them externally:
  1) image of the water shell (use opaque color)
  2) image of the contained structure
  3) composite the two images into a new combined image

Once you've got them, you can load them into GIMP, Photoshop, or ImageMagick
and composite the two images together manually. This method will
give you the most freedom in terms of material appearance and so on, but
it's a 3 step process instead of a single click.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 16, 2006 at 11:34:35PM +0300, Ivan Degtyarenko wrote:
>
> Dear All,
>
> did anybody see this kind of problem? I'm trying to plot high quality
> figure of the hydrated molecule. It's inside the water shell, thus I'm
> making the molecule itself opaque and the water around is transparent VDW
> surface. The basic snapshot is coming fine:
> http://www.fyslab.hut.fi/~imd/vmd/alanine_in_water.snapshot.jpeg
>
> but rendering does it wrong, it's drawing every single atom surface:
> http://www.fyslab.hut.fi/~imd/vmd/alanine_in_water.pov3.jpeg
> http://www.fyslab.hut.fi/~imd/vmd/alanine_in_water.tachyon.jpeg
>
> I'm using standard VMD settings for rendering and visualization. The
> initial file is a plain XYZ
> http://www.fyslab.hut.fi/~imd/vmd/alanine_in_water.xyz
>
> My platform is Linux SuSE 9.3, videocard ATI Radeon 9800 Pro.
>
> Thanks in advance for any reply!
>
> YT, Ivan Degtyarenko 

-- 
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