On Wed, 31 Mar 2010 15:00:34 -0400 "Clayton, Gina Martyn"
<[log in to unmask]> wrote:
> I am trying to colour a structure by B factor in Pymol. More
> specifically I am colouring conserved residues (value in b factor). I
> want to use 4 colours - say white, yellow, orange, red. However it
> seems that Pymol now only allows 3 colours to be used - I tried the
> script from the Wiki site, but Pymol will not accept the 4 rgb colours.
> Does anyone have an idea how I can colour with 4 colours (but not
> rainbow too confusing).
Say, your b-factor values range from 0-10, and your object is called
"protein", then you could do:
color white, protein
color yellow, protein & b > 2.5
color orange, protein & b > 5.0
color red, protein & b > 7.5
If you want to automate that process, then you need to write a script that
determines, the b-factor limits for the 4 colours based on the b-factors
present in your structure.
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821 Fax: 613-533-2497
<[log in to unmask]> http://pldserver1.biochem.queensu.ca/~rlc