VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 24 2006 - 11:56:51 CDT

Sergio,
  Actually there are quite a few ways to show embedded surfaces, but
transparency does indeed have limitations (for all programs). You can
either use the colorID method, or you could color by volume, and set
the color scale colors using a Hue/Intensity/Saturation ramp (to make them
change more obviously than using a simple RWB color scale for example),
and you can clamp the color scale data range values (see trajectory tab)
to get better control over how it is displayed. As far as the resolution
of the resulting image, the color by volume method is calculated either by
"nearest voxel" (the low quality option), or by trilinear interpolation
(the "medium" option). Better yet would be a cubic interpolation of some
sort, but at present the graphics boards aren't quite there yet, which is
why we don't have a "high" option. Ultimately, the resolution of the coloring
you get is determined by the combination of the original volumetric grid
resolution, and the largest texture map size your video card supports.
In the new versions of VMD, if your video card cannot load the full resolution
texture map, VMD will automatically downsample it to a lower resolution.
If you're getting a poor quality 3-D texturing result, the most likely
reason is due to limitations with your video card, so long as you're sure
that your original potential map data is high resolution...

  John

On Mon, Jul 24, 2006 at 11:28:07AM -0500, Sergio Urahata wrote:
> 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)
>
> Best,
>
> S.
>
>
> On 7/23/06, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> 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 akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > 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 http://dasher.wustl.edu
> ======================================================== 

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