This is to be answered by PDB people, who definitely read BB :) Would be nice to have a tool common between CCP4/Phenix and the PDB which sorts this out
Eugene On 30 Oct 2013, at 12:09, Andreas Förster wrote: > Dear all, > > this water discussion is flowing increasingly towards a place where I feel a > bit out of my depth. > > What is the convention for numbering water molecules? Is there preference > for: > > - putting waters into a separate chain (W for water or S for solvent)? > - splitting waters according to the peptide chains in the structure? > - appending all waters to chain A? > > > Thanks. > > > Andreas > > > > > On 30/10/2013 11:57, MARTYN SYMMONS wrote: >> At deposition the PDB runs a script that renumbers authors' waters >> according to a scheme based on the residue they are nearest from N to C >> terminus along each chain. This renumbering started when waters were >> assigned to macromolecular chains rather than getting a chain id of >> their own. I have failed to find the rationale explained in any PDB >> documents - but it could be motivated by this sort of consideration when >> waters from different chains or entries are to be compared. Having said >> that I do not know if there are any cases where this approach has >> successfully matched waters. .. >> >> However an associated step which is certainly a help is that, in the >> case of multiple chains, the crystal symmetry is applied to replace >> waters with their symmetry equivalent position if it is closer to a >> different chain. >> >> I believe a freely available program implementing a similar approach is >> WATERTIDY in CCP4 which might be a good place to start. It gives a >> pretty complete output, detailing residues actually H-bonded to the >> waters, and you could parse that for further analysis and comparisons. >> >> Best wishes. >> Martyn > > -- > Andreas Förster > Crystallization and Xray Facility Manager > Centre for Structural Biology > Imperial College London -- Scanned by iCritical.
