VMD-L Mailing List

From: Ivan Degtyarenko (imd_at_fyslab.hut.fi)
Date: Wed Aug 16 2006 - 16:50:44 CDT

Thanks a lot John once more, the second way was the right one. To anybody
interested, follow the instructions below, and after that, under Linux,
one can use one of ImageMagick utilities:

composite -dissolve 60 -gravity South molecule.tiff water_shell.tiff
-matte output.tiff

For the details:
http://www.cit.gu.edu.au/~anthony/graphics/imagick6/compose/#dissolve
http://www.imagemagick.org/script/composite.php

YT, Ivan

On Wed, 16 Aug 2006, John Stone wrote:

>
> 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