From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 27 2011 - 10:42:31 CDT

Brian,
  I agree with Axel's suggestion as the thing you should try first.
If that doesn't work well for you (e.g. if the time-varying selection
slows display down too much), then the next option would be to use a script
to rewrite the color scale with your own color scheme to get what you want.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 27, 2011 at 11:32:51AM -0400, Axel Kohlmeyer wrote:
> brian,
>
> On Mon, Jun 27, 2011 at 10:55 AM, Brian Puchala <puchala_at_wisc.edu> wrote:
> > Hi,
> >
> > I currently have a script that uploads data for each frame into "User" and
> > colors using that.  The data tells which atoms are grouped in a certain way
> > which varies from frame to frame.  I would like to give each group a
> > distinct color.  When there are more than about three or four different
> > groups the color scale does not provide enough contrast between different
> > groups, so I would like to be able to specify particular colors.  Is there
> > an atom attribute that changes from frame to frame but does not use the
> > color scale for coloring? Or a suggested work around?
>
> the in my opinion easiest way to address this is not by using a
> color gradient but rather using multiple representations and then
> the user field as a selection criterion. you can pick whatever color
> (or material or representation style) you want for the individual
> group and then use a "user == 1.0" or "user == 2.0" as the selection
> string. you need to activate the "update selection every frame" feature
> for it to work though.
>
> cheers,
> axel.
>
> >
> > Thank you,
> > Brian
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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