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
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