After deposition (my experience is with RCSB) you will get back a processed file to verify. See how the waters have been renumbered, and renumber in such a a way that your original scheme is easily identifiable but in keeping with whatever the renumbering was trying to achieve- e.g. your waters X1,X2,X3 could become A1001, A1002, A1003 and the symmetry related waters B1001, B1002, B1003. Discuss with the annotator to see how your waters can be renumbered in a recognizable way in keeping with requirements of the PDB conventions. Then in future depositions keep this same scheme (you may still need to renumber the original processed file each time). eab
Eckhard Hofmann wrote:
Hi all, during deposition of structures the water numbering is frequently changed. I would love to keep specific numbers for critical water molecules e.g. in an active site in related proteins (mutants, ligand soaks), to facilitate easier discussion in a manuscript. Is there a general agreement how to treat these? One way to deal with this is would be to use an arbitrary offset: A1-A233 protein A301 ligand A302 another ligand A401-404 4 special waters A500- general solvent Any input welcome ;-) All the best, Eckhard -- Prof. Dr. Eckhard Hofmann <[email protected]> Ruhr-Uni Bochum AG Proteinkristallographie, LS Biophysik, ND04/318 44780 Bochum Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762
