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I input the alignment in ESPript. Add the template PDB file and it makes a Bcol.pdb file where temperature factors are replaced my sequence similarity. I open this file in Pymol in Surface and color B-Factors as rainbow. Ivan On 12/7/11, Yuri Pompeu <[log in to unmask]> 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... >