On Thu, Aug 28, 2014 at 6:59 AM, CPMAS Chen <cpmasmit@gmail.com> wrote:

why there is apparent anomalous signal and I cannot identify any Br sites?

It's not immediately obvious to me why this would be the case - however, I would caution you that the estimation of anomalous signal in Xtriage isn't very robust. The newer builds will calculate CC(anom) if you give it unmerged data, which we think is more useful. It does seem weird that it would claim that the signal goes to 4Å when the anomalous map is flat, however.

As Nat pointed out, other atoms should have very weak anomalous signal diffracted at Br absorption peak (3.8e- for Br, versus 0.2e- for the sulfurs). In the difference map, I can clearly see some peaks at high sigma (> 6), but the anomalous difference map(they are all generated by phenix.refine or phenix.maps) is almost featureless, or the peaks has no overlaps. The anomalous difference gives the possible place of Br while the difference map gives the possible place of the whole ligand, and I assume there should be some overlaps between them. Am I right?

Yes, unless you have water molecules occupying the ligand density - but I think this would still be a pretty clear feature in the map.

-Nat