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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
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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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