On Thu, Jan 29, 2009 at 1:25 PM, Anastassis Perrakis <a.perra...@nki.nl>wrote:
> Dear all, > I was wondering what is the state of the art for this old dark art ... are > there any good servers / programs that allow to easily upload your own > sequence alignments or create a 'transparent' alignment (I want to see the > alignment first and not a total black box) and then allow you to write out > sequence conservation based either on identity or in e.g a Dayhoff matrix on > the B factor column for displaying it later in eg Pymol? > > To be clear I do not want a structural alignment, but mapping sequence > alignment of eg a family to a single structure of a family member. > ConSurf! You can submit your own Clustal alignment (the MSA program MUSCLE will also generate this file format). However, I was never able to visualize the PDB files it generates very well in PyMOL; I ended up extracting a different, simpler type of score (integers 1-9) from the results and applying that to the B-factor column instead of the score ConSurf writes.
