Hi Abhinav, On Thu, 29 Jan 2009 13:10:25 -0800, Abhinav Kumar <abhin...@slac.stanford.edu> wrote:
> Is there someway to select and show conserved residues when a bunch of > superimposed structures are loaded into Pymol? > And if so, can identical and similar residues be selected separately? I don't believe that there is a direct way to do it from the superimposition, but I commonly apply "external data" to the B-factor column of a PDB file for colouring purposes. For example, you could calculate the degree of sequence conservation at each residue and colour on that. I use the following scripts: http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/variability.py http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/seq_convert.py http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/data2bfactor.py See the pages: http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/ and http://pldserver1.biochem.queensu.ca/~rlc/work/pymol for more information. When you align the structures, if you use the "object=" keyword (or do it using the "align" menu) it will create an alignment object that you can save as a Clustal format file. This file can then be used to calculate the sequence variability. 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
