Dear Jacob, There are a lot of potential problems with ion validation, that make obtaining a reliable answer difficult. If you want to datamine ion validation results, you can use the ready-made WHAT_CHECK files in the PDBREPORT databank for original PDB files or in the PDB_REDO databank for their re-refined or rebuilt counterparts (note that PDB_REDO does not explicitly do anything with ions, yet). WHAT_CHECK uses the bond valence method to check for waters that should be ions and ions that should be other ions or water and mines the crystallisation conditions for hints of what could be there.
HTH, Robbie Sent from my Windows Phone ________________________________ Van: Keller, Jacob Verzonden: 6-3-2014 20:45 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] Validity of Ion Sites in PDB Dear Crystallographers, I was curious whether there has been a rigorous evaluation of ion binding sites in the structures in the pdb, by PDB-REDO or otherwise. I imagine that there is a considerably broad spectrum of habits and rigor in assigning solute blobs to ion X or water, and in fact it would be difficult in many cases to determine which ion a given blob really is, but there should be at least some fraction of ions/waters which can be shown from the x-ray data and known geometry to be X and not Y. This could be by small anomalous signals (Cl and H2O for example), geometric considerations, or something else. Maybe this does not even matter in most cases, but it might be important in others... All the best, Jacob Keller ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *******************************************
