Hi Alex.

> hello-
> i am new to pymol and am trying to figure out how to differentially
> color different chains (i.e. different proteins) in the structure i am
> viewing.  the structure i am working with is actually a structure of two
> proteins that were co-crystalized and i would like assign different
> colors to them.
> thanks for your help.
> alex dajkovic

As long as I know you can do that by creating copies of the same molecule. Do like this:

load molecule.pdb, mole
create copy, (mole)

Then assign different colors to each (for example):

color blue, mole
color red, copy

Finally show each chain separately:

show cartoon, (mole & c;A)
show cartoon, (copy & c;B)

(in the case you what a cartoon representation of chains A and B).

I hope that helps you.

Mario Sanches,  PhD Student
Protein Crystallography Group
São Paulo University, São Carlos Physics Institute
Phone:  +55 (16) 273 9868

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