COOT can do this very easily, just use the align and mutate command,
cheers, Matt.
On 23/06/2011 10:42, Simon Kolstoe wrote:
Dear ccp4bb,
One of my colleagues is interested in how a certain protein differs between species. He's
done a blast search, collected all the aligned sequences, and "emailed them to the
crystallographer to tell him the implications of the sequence changes".
Although I am not at all confident that I can predict any implications based
upon sequence differences, I thought I could at least have a try by mapping the
different species sequences onto the existing structure and then regularising
it just to see what happens (and then perhaps looking at buried surface area,
electrostatics, subunit interfaces etc.).
I know the program chainsaw can mutate the sequence based on an alignment,
however I can't stop it pruning non-conserved residues. Does anyone know of
another program that I could use to do this step?
Similarly if anyone knows other software tools/methods I could use to try and
work out the implications of sequence changes I would be grateful for advice.
Thanks,
Simon
--
Matthew Bowler
Structural Biology Group
European Synchrotron Radiation Facility
B.P. 220, 6 rue Jules Horowitz
F-38043 GRENOBLE CEDEX
FRANCE
===================================================
Tel: +33 (0) 4.76.88.29.28
Fax: +33 (0) 4.76.88.29.04
http://go.esrf.eu/MX
http://go.esrf.eu/Bowler
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