Re: [phenixbb] anomalous difference map

On Sat, Mar 26, 2011 at 11:57 AM, Nathaniel Echols wrote:

On Sat, Mar 26, 2011 at 9:45 AM, Jason 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

====================== Jason Structural Biology Department University of Pittsburgh ======================