[phenixbb] anomalous difference map

Nathaniel Echols nechols at lbl.gov
Sat Mar 26 09:57:07 PDT 2011

On Sat, Mar 26, 2011 at 9:45 AM, Jason <phenix.upitt at 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

> 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.


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