Hi all,
Mmmm...
Let me kow if I am wrong about this, but as far as I can say the problem with stereochemistry (Ramachandran plot) is not necessarily related to a bad sequence alignment...
(You could have a very bad stereochem [maybe as a result of a bad/poorly refined model] and a good rama plot. Modeller is more suceptible to give you the inverse scenario: a really good stereochem, without regard of the quality of your alignment...)
there are several tools more suited to evaluate your alignment and as a result, your coordinate asssignment (they evaluate the coordinates of your final model).
I think that Prosa2003 and profile3D are a couple of examples.
Hope this helps,
Luis
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---------- Original Message ----------- From: rajesh rengaraj rajesh_rengaraj@yahoo.co.in To: inbios groups inbios@yahoogroups.com, modeller modeller_usage@salilab.org, groups mtech biopearls@yahoogroups.com Sent: Tue, 15 Mar 2005 09:00:59 +0000 (GMT) Subject: [modeller_usage] Regarding manual protein sequence alignment
> Hi friends. > > I need help from our groups regarding the Protein > manual sequence alignment.I modelled a protein which > shows low Ramachandran plot validatity in order to > increase this i have to do the manual alignment.I dont > know what are the procedure for this and how to do > this, whether it is depends upon the physico-chemical > properties of amino acids or any other else. > > So Kindly do the needful. > > Take care. > > ________________________________________________________________________ > Yahoo! India Matrimony: Find your life partner online > Go to: http://yahoo.shaadi.com/india-matrimony > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage ------- End of Original Message -------