VMD-L Mailing List

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Mon Sep 20 2004 - 16:29:50 CDT

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
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