Efficient way of showing residue conservation-thank you everyone

From: Yuri
Date: 8 December 2011 14:20



On Thu, 8 Dec 2011 09:19:57 +0000, Mads Gabrielsen wrote:

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






On 08/12/2011 05:26, "Yuri Pompeu"  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...

--
Yuri Pompeu