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 -- Open WebMail Project (http://openwebmail.org) ---------- 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 -------