VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 27 2004 - 09:29:40 CDT

Hi Margaret,
  Depending on the size of the solvent box, one can usually make a Surf
or MSMS representation that does this sort of thing nicely. Another
option would be to try something like the delaunay triangulation
script here:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/delaunay_triangulate/

Surf and MSMS are probably simplest to try first.

  John

On Fri, Sep 24, 2004 at 11:48:09AM -0400, Margaret Shun Cheung wrote:
>
>
> Hi, John and other VMD maestros,
> Thanks. I wonder how to make a thick slab out of a box of solvent that is
> able to show the rim of holes in the solvent.
> Thank you very much.
> Margaret
>
> On Mon, 20 Sep 2004, John Stone wrote:
>
> >
> > Margaret,
> > The easy way of doing something like this is with the use
> > of a complex atom selection such as:
> >
> > Cut out a 10A sphere around atom index 4712:
> > not (within 10 of index 4712)
> >
> > Cut out a 10A radius sphere around atom index 4712, and cut out atoms
> > with X less than 3:
> > (not (within 10 of index 4712)) and x >= 3
> >
> > There are various examples of this here:
> > http://www.ks.uiuc.edu/Research/vmd/current/ug/node76.html
> > http://www.ks.uiuc.edu/Research/vmd/current/ug/node84.html#5063
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Mon, Sep 20, 2004 at 12:09:59PM -0400, Margaret Shun Cheung wrote:
> > > Hey, VMD wizards,
> > >
> > > I'd like to carve a spherical big bubble (diag ~ 15\AA)
> > > out of a box of solvents. And make a snapshot of its
> > > crosssection with the rest of solvent molecules for presentation.
> > > Any idea of how could do this, uh effortlessly?
> > > Thank you for your time.
> > >
> > >
> > > Sincerely,
> > > ----------------------------------------------------------------
> > > Margaret S. Cheung, Ph. D. | IPST UMCP Tel: (301)405-4892
> > > Postdoctoral Fellow | IPST UMCP Fax: (301)314-9404
> > > IPST Room 2117 | NCBI NIH Tel: (301)402-9527
> > > University of Maryland | http://glue.umd.edu/~mscheung
> > > College Park, MD 20742-2431 | email: mscheung_at_glue.umd.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
> >
>
> Sincerely,
> ----------------------------------------------------------------
> Margaret S. Cheung, Ph. D. | IPST UMCP Tel: (301)405-4892
> Postdoctoral Fellow | IPST UMCP Fax: (301)314-9404
> IPST Room 2117 | NCBI NIH Tel: (301)402-9527
> University of Maryland | http://glue.umd.edu/~mscheung
> College Park, MD 20742-2431 | email: mscheung_at_glue.umd.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