On Thu, Jan 29, 2009 at 1:25 PM, Anastassis Perrakis <[log in to unmask]> 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.