Given that the water and the barium seem to have the same electron density on image electron…png I’d 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_Crystallography_Fig_12-33_AandB.htm

Similar but somewhat different situation of correlated occupancies

http://www.ruppweb.org/garland/gallery/Ch13/pages/Biomolecular_Crystallography_Fig_13-04.htm

From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Dhanasekaran Varudharasu
Sent: Monday, June 13, 2011 9:48 AM
To: [log in to unmask]
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