[phenixbb] anomalous difference map

Jason phenix.upitt at gmail.com
Sat Mar 26 10:22:06 PDT 2011

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

> 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
> 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

Structural Biology Department
University of Pittsburgh
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