Coot can do that. You can use lsq to overlap the whole atoms of ligands.
Another way is using LigAlign in Pymol.
Good luck!
leo
rui wrote:
> Hi, All
>
> I have dozens of complex structures ( protein + ligand ) and want to
> align the structures based on the ligand. Does anyone know such kind
> of program? Or if can get the information around the ligand site, that
> would be even better.
> Thanks.
>
> R
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