Liu,
Your problem deals essentially with side chains. You have to know that all programs of homology modeling have difficulties for prediction of side chains and results are often bad... Basically, at the biginning, programs choose conformation of side chains of templates in conditon that the same residuse are aligned. If it is not the case, the side chain is placed and is minimized. So, it is logical whether your side chains are different between your models because the minimization depends on the local environnement.
I hope you have understood what i had tried to explain...
With regards, Mickaël
On Wed, 24 Mar 2004, Binbin Liu wrote:
> Hi there, > I got one hunderd models. The side-chain torsion angles of the interesting > residues are vary. Does anybody know why. Does MODELLER calculate the torsion > based on some rules or it is by chance. > > > Cheers > > > BinBin > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage >