I believe Charlie Bond's ALINE (http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/) will let you make a nicely coloured sequence alignement, and then write out a Pymol script which will colour the surface by conservation.
Mads -- Mads Gabrielsen, PhD Institute of Infection, Immunology and Inflammation College of Medical, Veterinary and Life Sciences University of Glasgow Room B216 /L303 GBRC 120 University place G12 8TA Phone: 0141 3307264 / 6180 E-mail: mads.gabriel...@glasgow.ac.uk On 08/12/2011 05:26, "Yuri Pompeu" <yuri.pom...@ufl.edu> wrote: >I once saw a figure showing the protein as surface, but instead of having >it coloured by atom type >or potential, it was shown by percent conservation in the family. >Something like red highly conserved, all the way to white, not conserved >at all... >Now, I assume the figure was done by uploading aligned sequnces of >several members of a family, and the colouring >the generated surface accordingly. >Does anyone know a way to do this more elegantly than what I tried doing? >ps. I quit colouring them manually after I remebered my protein was 407 >aa long...
