Well, let's see. Just for speed, let's use sasurface:

 isosurface sasurface map property groupid


GROUPID is an atom property that identifies the amino acid residue by number. See the documentation for that. Yes, you could set up your own color scheme at the same time:

isosurface sasurface map property groupid colorscheme "user=[xff0000],[x00ff00],[x0000ff]"

for example, but with 26+ colors. Then you also want to make sure you define the range:

color isosurface range 1 26  # whatever matches the number of colors you have

Bob

On Fri, Nov 26, 2010 at 9:36 AM, Alexander Rose <alexander.rose@weirdbyte.de> wrote:
Hi,

I'm trying to color the molecular surface by the color of the underlying atoms/residues.

my naive approach (not what I want, but colorful):

select protein;
color amino;
isosurface ignore {not protein} select {protein} molecular map property color translucent;


if I understand it correctly this happens: the colors of the atoms are onto the default colorscheme 'roygb' by which the isosurface is then colored. to achive what i want i need to create a 'color' colorscheme?



Best
Alex

------------------------------------------------------------------------------
Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
Tap into the largest installed PC base & get more eyes on your game by
optimizing for Intel(R) Graphics Technology. Get started today with the
Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
http://p.sf.net/sfu/intelisp-dev2dev
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users



--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900