I do not think we "are there yet" especially when partial occupancies come into play. Then it is a real mess. We always collect "all available evidence" (databases, CSD, PDB seraches, anomalous, distances, geometry, fluorescence spectrum at beamline etc.) and then try to make the best guestimate .. Na+ is and will be always uneasy.
Jan D. On Tue, Jun 14, 2011 at 11:34 PM, Jacob Keller <j-kell...@fsm.northwestern.edu> wrote: > Dear Crystallographers, > > While I acknowledge that assigning solvent/ions/waters to blobs of > density is prone to subjectivity, does anyone here know of any > attempts to rigorously assign solvent blobs based on their > characteristics, e.g., nearby residue types, height of peak, etc? I > wrote previously to the BB about distinguishing Na from water, and got > the message that it is far from simple to distinguish the two, but > what about others? I guess the question driving this email is to what > degree can one trust solvent assignments in the pdb? Does it have to > be a case-by-case evaluation? Does anyone know of a good publication > addressing this dilemma? > > Jacob > > -- > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > cel: 773.608.9185 > email: j-kell...@northwestern.edu > ******************************************* > -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
