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 ________________________________ From: Joel Sussman <[email protected]> To: [email protected] Sent: Wednesday, 30 October 2013, 6:49 Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs For detailed examination of this topic, see: Koellner, G., Kryger, G., Millard, C. B., Silman, I., Sussman, J. L. & Steiner, T. (2000). Active-site gorge and buried water molecules in crystal structures of acetylcholinesterase from Torpedo californica. Journal of Molecular Biology 296, 713-735. http://www.ncbi.nlm.nih.gov/pubmed/10669619 best regards, Joel On 30 Oct 2013, at 01:35, Ed Pozharski <[email protected]> wrote: http://www.ccp4.ac.uk/html/watertidy.html > > >On 10/29/2013 04:43 PM, Elise B wrote: > >Hello, >> >>I am working on a project with several (separate) structures of the same >>protein. I would like to be able to compare the solvent molecules between the >>structures, and it would be best if the waters that exist in roughly the same >>position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. >> >>What would be the best strategy for re-numbering the water molecules such >>that those with similar coordinates in all the structures receive the same >>residue number? I'd appreciate any suggestions. >> >>Elise Blankenship >> >> > >-- >Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > Julian, King of Lemurs >
