VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 20 2004 - 16:35:03 CDT

Margaret,
  Perhaps I'm not understanding what you have in mind, but you can use
two rep + atom selection pairs to color the atoms on the two sides
of a boundary differently, which is what I had though you were trying
to do. (i.e. one is the "not" of the other in VMD atom selection parlance)
If you only want to highlight the boundary itself, and not the atoms that
fall on either side, then you'd want to use a surface representation of
one kind or another to do this. There's actually an VMD plugin
written by a group in France for this exact purpose, but it isn't generally
available quite yet, it'll be widely announced when they've worked out the
licensing issues on it.

  John

On Mon, Sep 20, 2004 at 05:29:50PM -0400, Margaret Shun Cheung wrote:
>
> Hi, John,
> Thank you for the email. Using different colors to differentiate
> contents inside the hole probably couldn't meet what I had in mind.
> Is there a way just to color the "boundaries" defined by such
> radius? Thank you.
> Margaret
>
> On Mon, 20 Sep 2004, John Stone wrote:
>
> >
> > Margaret,
> > You can use multiple atom selections to color the interior atoms
> > differently than the others, by specifying different ColorID's for the
> > two selections, just as an example. There are lots of tricks for
> > doing things like this, experimentation with the color by ColorID
> > and varoius selections is probably a good way to get started.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Mon, Sep 20, 2004 at 03:46:29PM -0400, Margaret Shun Cheung wrote:
> > >
> > >
> > > Hi, John,
> > > Thank you for the suggestions. I am seeing a hole in a box
> > > of solvents. Is it possible
> > > to "color"
> > > the shell of this bubble, so it can be visually more appealing?
> > > Thanks.
> > > 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
> >
>
> 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