Hii Ruchi!! well.. you can do loop refinement for further refining process. and another thing you can use minimization techniques like MD, where you can give a slight heating up of protein to shake the structure a bit, and then let it relax to attain favorable conformation. Hope it helps.. Cheers! Monika

On Thu, 4 Sep 2008, rsachdeva@imtech.res.in wrote:

> Dear All, > > I built 200 tetrameric models of my protein using 2 templates. I selected best > model as the one having the least DOPE score. On ssessing the stereochemical > quality of the model, I found that it had 28 outliers residues (phi, psi), that > were lying in disallowed regions of Ramachandran plot. Most of these residues > are functionally important and hence can not be ignored. Will it be fine to > select each of these residues and model them using loop modelling? > > Or can anyone please suggest me some other (better) way of fixing such bad > residues? > > With Regards > > Ruchi > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >