Re: [PyMOL] coloring based on sequence identity

[Robert Campbell]

Dear Morri,

On Fri, 22 Aug 2008 13:35:32 -0700, Morri Feldman
morrifeld...@gmail.com wrote:

 Dear Rob,
 
 I'm interested in using your variability script with a substitution matrix.
 Would you please send me an example of a substitution matrix file?  Thanks
 for writing such a useful script.

Sure.  Attached are a couple of matrices.  One is a blosum80 matrix and
one is a hydrophobicity matrix.  I think I found them at:

http://www.techfak.uni-bielefeld.de/bcd/Curric/PrwAli/nodeD.html
http://www.techfak.uni-bielefeld.de/bcd/Curric/PrwAli/nodeE.html

You should be able to easily create your own following those examples.

Cheers,
Rob
-- 
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: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc


blosum80.mat
Description: Binary data


hydrophobicity.mat
Description: Binary data

Re: [PyMOL] coloring based on sequence identity

[Martin Höfling]

Am Dienstag, 26. Juni 2007 schrieb Eva Vanamee:
 Hi,

 I'd like to color a molecule based on its sequence similarity to another
 molecule.
 Can this be done in Pymol?

If you can quantify similarity in a number you can write it into the 
b-factors of the atoms and then color it by them.

Best
Martin

-- 
Wenn Theorie und Realität nicht übereinstimmen, muß entweder die
Theorie oder die Realität geändert werden. Das erste nennt man
Wissenschaft, das zweite Religion. [Achim Stoesser, 12.8.1999]