PyMOL Molecular Graphics System

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=20
b-factors of the atoms and then color it by them.

Best
	Martin

=2D-=20
Wenn Theorie und Realit=E4t nicht =FCbereinstimmen, mu=DF entweder die
Theorie oder die Realit=E4t ge=E4ndert werden. Das erste nennt man
Wissenschaft, das zweite Religion. [Achim Stoesser, 12.8.1999]

* Martin Höfling <martin.hoefling@...> [2007-06-27 01:33] wrote:
> 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.

I have a script:

  http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/variability.py

that takes a FASTA or Clustal format sequence alignment and calculates
the variability of the sequence at each position by:

   variability = (# different a.a.) / (frequency of the most common a.a)

The output can be either the complete set of information (a set of
columns of data showing each sequence, the number of different a.a, the
number of the most common a.a., the frequency of the most common a.a and
finally the variability) or a simple file that can be imported into
PyMOL via my data2bfactor.py script to change the B-factor into the
variability. Then one can color on that property.

The variability.py script depends on having biopython installed and it
calls my seq_convert.py script as well. See:

  http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/seq_convert.py

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: 613-533-6821            Fax: 613-533-2497
<robert.campbell@...>    http://pldserver1.biochem.queensu.ca/~rlc

Dear Morri,

On Fri, 22 Aug 2008 13:35:32 -0700, Morri Feldman
<morrifeldman@...> 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: 613-533-6821            Fax: 613-533-2497
<robert.campbell@...>    http://pldserver1.biochem.queensu.ca/~rlc