VMD-L Mailing List

From: Margaret Shun Cheung (mscheung_at_numipst.umd.edu)
Date: Fri Sep 24 2004 - 10:48:09 CDT

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
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