* Martin Höfling <martin.hoefl...@gmx.de> [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.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
