Thank you all for quick replies. The issue has been solved by using
sortwater and a little manual editing. Using PDBe could be a easier
way. Next time I may try it.

Best,
Zhiyi

On 7/31/12, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote:
> 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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