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Re: [ccp4bb]: how to prepare a structure-based sequence alignment



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> Recently, I want to prepare a structure-based-sequence-alignment figure, but 
> I don't know how to do it. In addition, how should I deal with those 
> residues that are of similar physicochemical properties but are not of equal 
> positions.

if you have LSQMAN available, this is a breeze. see the example
at http://xray.bmc.uu.se/usf/lsqman_man.html#H6 (and get the
macro from ftp://xray.bmc.uu.se/pub/gerard/omac/align.lsqmac).
this will give you the structure-based sequence alignment of
the structurally conserved parts. parts of both sequences that
are not conserved in the structure will not be aligned by
sequence either

--gerard

******************************************************************
                        Gerard J.  Kleywegt
    [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                Biomedical Centre  Box 596
                SE-751 24 Uppsala  SWEDEN

    http://xray.bmc.uu.se/gerard/  mailto:gerard@xray.bmc.uu.se
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