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 > >