Hi Jason,

Can anybody go through it for me please, or there are other handy programs that can make anomalous difference map?

phenix.maps (from command line or GUI) is THE tool to do this task. phenix.refine outputs this map too, as yourself or Nat mentioned already. If the anomalous difference map doesn't show anything, then I guess the following are among the possibilities: 1) there is nothing to show, 2) there is something not right with the data itself, 3) you feed incorrect data into the program or run the program incorrectly.

It depends on the ligand, I guess. If it's large enough and actually
bound, it should be detectable in the Fo-Fc map - this would be a good
sanity check to make sure that the anomalous map generation is working
properly.

Unfortunately my ligand is fairly small, about 12 atoms.The Fo-Fc map won't be that helpful.

I'm quite puzzled about this... We use Fo-Fc maps to find water oxygens (one single atoms)! Why one would think that 12 molecule is too small to see it in Fo-Fc map? Am I missing something?

If you like, you can send me the data and model files and I will try myself.

Pavel.