On Sat, Mar 26, 2011 at 11:57 AM, Nathaniel Echols <nechols@lbl.gov> wrote:

On Sat, Mar 26, 2011 at 9:45 AM, Jason <phenix.upitt@gmail.com> wrote:
> 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.

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

> 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.

XDS is the only program that is able to process my data (small oscillation angle and huge data file). On the other hand I am pretty sure xds is doing what it's supposed to do. I was more thinking of another program to generate anomalous map. Since it's phenixbb, probably it's not the right place :)

Also: run Xtriage and look at the plot of anomalous signal vs. resolution.

-Nat