The old fashioned water tidy will try to assign matching (non-standard) names to matching H2Os which is useful for analysis of structural waters, but cannot be deposited.
I think coot has a tool to move waters to be near the protein but maybe that isn't all you want. Why not start deposition and use PDBe renaming then download the pdb file again to continue refinement?
Eleanor
On 30 Jul 2012, at 09:27, Zhiyi Wei wrote:
> Dear all,
>
> I have a refine structure with 8 ncs copies and several hundreds of
> water molecules (which was put in one chain). Now I try to separate
> these molecules by renaming to the chain id of each adjacent protein
> molecule. I know RCSB can do this during deposition process. Do anyone
> know a program can do a similar task? Many thanks!
>
> Best,
> Zhiyi
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