Well - years ago I wrote a program called watertidy to do just this - but it asigned waters as OH0 OH1 OH2 with a according to what atom it was H bonded too, and those names are not now permitted..
My way now is to read in a completed homologous structure - use SSM to fit it over the new one - extract the HOHs from structure 1 - add them to structure 2 - do some refinement and use COOT to decide which ones are valid - the "density fit" picture shows wonderful red bars for wrong'uns - then add more again using coot.. Eleanor On 30 October 2013 06:49, Joel Sussman <joel.suss...@weizmann.ac.il> wrote: > 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 <epozh...@umaryland.edu> 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 > >
