Hi Camille The Espript server is the easiest way I know. Go here
http://prodes.toulouse.inra.fr/ESPript/cgi-bin/ESPript.cgi choose Execute then Expert mode. SUpply an alignment and a supplementary pdb file then execute. You get back an annotated alignment + the pdb file with a conservation score in the b-factor column. The only trouble can be making that the top sequence in your alignment matches exactly the sequence of the structure (no missing loops etc). You can read this new pdb file into Pymol and colour easily with Robert Campbell's script color_b.py which you get here http://adelie.biochem.queensu.ca/~rlc/work/pymol/ Good luck Daniel On Fri, 2004-05-21 at 15:28, cami...@mrc-lmb.cam.ac.uk wrote: > Hello PyMol community! > > is there any way to display sequence conservation on the surface of a > protein? > i.e. to use the info I have in a sequence alignment. > > do I have to do this by hand? > > Thanks, > Camille > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: Oracle 10g > Get certified on the hottest thing ever to hit the market... Oracle 10g. > Take an Oracle 10g class now, and we'll give you the exam FREE. > http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4414 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K.
