VMD-L Mailing List

From: Sergio Urahata (surahata_at_dasher.wustl.edu)
Date: Mon Jul 24 2006 - 12:21:32 CDT

Thank you again, Axel and John.

I am looking into your suggestions. I am using
version 1.8.4 under Windows XP with an ATI X700 video card.

Regarding the resolution, I will re-run my code again with
an increased number of grid cells. This may do the trick (I would need
to do this anyway because there are way to many zero's
on it, leading me with an useless huge file). I must say that even
the medium resolution is not bad since the color range is
very clear on the clipping plane. My only grip is the color of this plane
which is always blue (using any color ID/User coloring option),
red (with Charge/Volume) or "multicolor" (with Pos). White would
be the best way to see the cutting layers.

S.

Obs. Axel, I do not mind sharing this data but right now the file
       uses almost 80MB. As soon as I get it smaller, I can upload it
       there.

On 7/24/06, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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
> > ========================================================
>
> --
> 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
> 

-- 
========================================================
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
========================================================