Re: [ccp4bb] manipulation of water molecules in pdb files
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
Re: [ccp4bb] manipulation of water molecules in pdb files
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
[ccp4bb] manipulation of water molecules in pdb files
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
Re: [ccp4bb] manipulation of water molecules in pdb files
Dear Zhiyi, I think that sortwater (http://www.ccp4.ac.uk/html/sortwater.html), will do something along what you want. Remember to read the documentation ;-) Best regards, Folmer 2012/7/30 Zhiyi Wei ustcwebri...@gmail.com 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 -- Folmer Fredslund
