VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 20 2004 - 13:23:14 CDT

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
> ---------------------------------------------------------------- 

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