On Sat, Mar 26, 2011 at 9:45 AM, Jason
I was hoping to identify the ligand binding position by resolving the anomalous map first. Shouldn't this be the procedure to locate ligand?
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.
I know CCP4 can also generate anomalous difference map. But I myself have never done it (I googled online and found it not that straight forward). Can anybody go through it for me please, or there are other handy programs that can make anomalous difference map?
You don't need to use CCP4 to make the map, just to process the data - i.e. use MOSFLM/SCALA (xia2 will automate this), or you could also try HKL2000, then use that as input for Phenix. But I doubt this is going to give you a different answer. Also: run Xtriage and look at the plot of anomalous signal vs. resolution. -Nat