Dear Uma, These look like waters to me. Generally, for ion detection you can use WASP or WHAT_CHECK and for validation of built ions you can use the CheckMyMetal server.
Cheers, Robbie Sent from my Windows Phone ________________________________ Van: Uma Ratu Verzonden: 24-11-2013 1:15 Aan: [email protected] Onderwerp: [ccp4bb] Water or ion Dear All: I use Coot to check water molecules in my model. Most of them are in good coordinates for water. Some of these waters have unusual coordinates. For example, one is in the H-bond distance with 2 nitrogen and 2 oxygen of protein residues, plus one oxygen from ligand (W_230.jpg), and the other is in the H-bond distance with 3 nitrogen, 1 oxygen of protein residue, plus one water(W_300.jpg). Would you advice if these molecules are water, or something else, ions? I tried Coot - "highly coordinated water", and "check/delete water". The program does not pick up anything unusual. Thank you Uma
