VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Jul 24 2006 - 11:43:42 CDT

On 7/24/06, Sergio Urahata <surahata_at_dasher.wustl.edu> 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.

you may want to look into pymol for doing that. i saw some
interesting pictures. i've been playing with embedding multiple
isosurfaces into one another with using transparency several
times (using OpenDX which is much better suited for grid data),
but it was rarely useful. the best that worked way either
'peeling off' parts of the isosurface to reveal the underlying surfaces,
or have one wireframe, one transparent and one opaque surface
at the most..

>
> 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.

what version of VMD are you using and on which platform.
can you make an example data set available?
(best by joining the public VMD project on
biocore and uploading your data to the biofs).

> 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)

the volume slice representation has been a bit of a stepchild
for a while now. you should get a reasonably good quality when
using the Volume colorization. alternatively, using Charge seemed
to work well. you can set the data values used for the color range
in the trajectory tab and the color scale type in the color menu.

regards,
    axel.

>
> Best,
>
> S.
>
>

> --
> ========================================================
> 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
> ========================================================
>
> 

-- 
=======================================================================
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.