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
--
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...
--
Yuri Pompeu
