Hi Yuri, > 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...
PyMOL can do this pretty easily now. First you need to calculate an alignment, then you need to do the coloring. The alignment step is done like this: align protA, protB, object=aln I then wrote a script to automate the coloring of residues by conservation in the sequence alignment. You can find the script on the PyMOLWiki, here http://pymolwiki.org/index.php/Color_by_conservation. The script does a couple other useful things like showing the conservation not only by color but by cartoon putty radius, and expanding the alpha-carbon conservation to surface colors. You can find an example to copy/paste into PyMOL on that page. Hope this helps. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
