From: Sergio Urahata (
Date: Mon Jul 24 2006 - 11:28:07 CDT

Thank you for the message, Axel.

The reason I was playing with the transparency option
is related to the way the data is distributed. If I just use color ID
for each volume, it is not possible to see these distinct regions, since
they are embebbed in each other.

Your second suggestion solves this problem but there is one
bug on the Clip Tool. The "Distance" bar does not move and
the number on its side does not change, no matter
whether the "Keep Aligned with Screen" is selected or not.

I then tried to render the volumes using Volume Slice and
the result is much better indeed. Do you know how to control
the color of the slicing plane ? Also, is there a way to increase
the quality of the projection ? (there only "low" and "medium" quality
on the menu)



On 7/23/06, Axel Kohlmeyer <> wrote:
> On Sat, 22 Jul 2006, Sergio Urahata wrote:
> SU> Hi all,
> hi sergio,
> SU> I have one PLT file which represents a 3D grid of volumetric data.
> SU> VMD allows to render only specific isovalues, which is great.
> SU> Would it be possible to set different colors for specific isovalues ?
> yes, you just create multiple isovalue representations and
> assign a different color to each of them (via ColorID colorization).
> SU> This way, one could show where to find higher densities (or whatever the
> SU> mean each cell has) hence adding an interesting function for
> SU> the "transparent" material option.
> i don't think so. the colors on the 'outside' would tint
> whatever is 'inside'. what you may want to look into would
> be a volume slice with Volume colorization, perhaps in
> combination with multiple isosurfaces and a clipplane.
> regards,
> axel.
> SU> I have selected many "Coloring" methods and "Volume" was the only
> SU> one which changed the surface color (but still does not use
> SU> the isovalues).
> SU>
> SU> Thank you,
> SU>
> SU> Sergio
> SU>
> SU>
> --
> =======================================================================
> 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.

Sergio Urahata, Ph.D.
Biochemistry, Box 8231          Phone: (314) 362-4198(O)
Washington University                  (314) 454-9209(H)
660 South Euclid Ave              Fax: (314) 362-7183
St. Louis, MO 63110