I have a slightly different answer using (almost:) only PyMOL commands:

# take 1acb as example
fetch 1acb, async=0
import numpy
# center is [x0,y0,z0]
alldist = []
iterate_state 1,  1acb, alldist.append(numpy.sqrt(numpy.sum([(x-x0)**2,(y-y0)**2,(z-z0)**2])))
# assign dist to b-factors!
di = iter(alldist)
alter 1acb, b=di.next()
spectrum b, rainbow, 1acb

The distance computation line is awkward. I thought of using distance() command to replace it. It is also much faster to use distance(). But I failed to dig distance values out of the object generated by distance(). Anybody knows how to do that?


On 28.07.2011 5:06, Thomas Holder wrote:
Hi Robert,

you can set the distance between each atom and the center as b-factor, and then use spectrum (or spectrumany [1]) for coloring.

I wrote a small python script that will do that, see attachment.

Example (in PyMOL command line):

run distancecoloring.py
centerdistance2b (all)
spectrum b, blue_white_red, (all)


[1] http://pymolwiki.org/index.php/Spectrumany

On 07/28/2011 04:29 PM, Muench, Robert wrote:
Dear community,

I was searching the internet for several days now to find out how to
perform a distance dependent coloring in pymol.

The idea is to color the surface of a viral (spherical) structure. I
would like to define the xyz-coordinates of the center of the viral
structure an color all residues with a gradient depending on the
distance from these xyz coordinates.

Can anyone please help me out?

All the best


*Robert Münch***


Dipl. Biologist / PhD-Student


Federal Institute for Vaccines and Biomedicines

Division of Medical Biotechnology

Section 6/5 - Viral Gene Transfer Medicinal Products

63225 Langen, Germany

Phone: +49-6103-77-4222

Fax: +49-6103-77-1255

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