Given that the water and the barium seem to have the same electron density on image electron png Id look careful at relative density levels, occupancies, B-factors etc. Often the situation becomes clearer during later stages of refinement.
Peripherally, I also do not exactly understand the difference between split barium and individual barium. Are two half occupied bariums necessary non-individuals? The split term in crystallography colloquially relates to multiple conformations of the same entity, which in case of side chains does require constrained occupancies. This is not necessarily so for isolated atoms, where the term imho looses its meaning. However, constrained occupancies can be imposed on individual atoms by split side chain conformations. I have some examples in the figure library http://www.ruppweb.org/garland/gallery/Ch12/pages/Biomolecular_Crystallograp hy_Fig_12-33_AandB.htm Similar but somewhat different situation of correlated occupancies http://www.ruppweb.org/garland/gallery/Ch13/pages/Biomolecular_Crystallograp hy_Fig_13-04.htm BR From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Dhanasekaran Varudharasu Sent: Monday, June 13, 2011 9:48 AM To: [email protected] Subject: [ccp4bb] About heavy atom split Dear experts, We have solved one protein structure with barium as a heavy atom using SAD technique. But in the final refinement one barium site shows split. But the distance between the two positions is 3.8 Å. Please give your valuable comments and suggestions to conclude whether it is due to split or due to the occurrence of two individual barium atoms. Herewith I have enclosed the image files containing the electron density map at 1.00 sigma level and the anomalous map at 4.00 sigma level for your reference. with regards Dhana
