VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 05 2009 - 10:28:42 CDT

Hi,
  When your density map is generated you should see some messages like
this in the VMD text console:
  Info) Analyzing Volume...
  Info) Grid size: 284x284x284 (349 MB)
  Info) Total voxels: 22906304
  Info) Min: 0.000000 Max: 0.603308 Range: 0.603308
  Info) Computing volume gradient map for smooth shading

Be sure to select an isosurface representation with an isovalue that
falls within the min/max range, typically toward the very lowest end of
the range for this type of rendering, or you won't see anything.
For the example above, I'd recommend using an isovalue of 0.01 or so.

Once you've got that, then you'll want to use a transparent material,
and you can then render the image with Tachyon, or one of the other
renderers, and get a nice figure like the STMV figure.

I should also warn that the volmap command can generate very large
datasets very quickly if you use a high-resolution grid spacing on
a large molecular complex. While you're doing your testing, I'd
suggest starting with a coarse grid spacing like 2A and
work your way toward progressively finer grids so you don't run yourself
out of memory. Each halving in grid spacing multiplies memory usage
by a factor of 8x.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 05, 2009 at 11:16:45PM +0800, ?????? wrote:
> Thank you, John. I tried volmap tool in VMD. And the the value for
> "selection" is water, volmap type is density. Other values are default
> values. But I still can not get the picture similar to STMV. Are there any
> other parameters I have to modify?
>
> Best,
> Wenchang
>
> 2009/5/5 John Stone <johns_at_ks.uiuc.edu>
>
> >
> > Hi,
> > The water box for STMV was created with the "volmap" command
> > (or the GUI interface), with the "density" map type, if I recall.
> > The surface of the capsid was generated via MSMS one fragment at
> > a time, IIRC.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, May 05, 2009 at 09:31:33PM +0800, ?????? wrote:
> > > Dear all,
> > > Does anyone konw how to make images like STMV on VMD website?
> > > (
> > http://www.ks.uiuc.edu/Gallery/Science/Structure/tn/cover_fig_st.jpg.html<
> > http://www.ks.uiuc.edu/Gallery/Science/Structure/tn/cover_fig_st.jpg.html>
> > > )
> > > I am very interested in making the water box and ions in this picture,
> > which
> > > is beautiful and proteins can be seen clearly.
> > > Thank you.
> > >
> > > Best,
> > > Wenchang
> >
> > --
> > 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
> > 

-- 
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