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
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