3.  Calculating the phases

We are going to solve the structure using only the one derivative.   You can use both derivatives to get a (better?) estimate for the phases.  The one trick you will need to know is that you should use the phases calculated here to find the second derivative site (from data set 123) by cross-difference fourier to ensure that you have the same (arbitrary) origin in both cases.  (Correlation of origins is a significant problem in multiple isomorphous replacement.)

First, we will use this solution for the Br site in derivative data set 124:  ccp4_generated.sdb  As you can guess, it is the same as the one we found in the CCP4 example, and it is absolutely equivalent to the one that CNS finds, but for convenience in displaying the map with the coordinates on deposit at the pdb, we will use this solution.

The first thing to do is to calculate Single Isomorphous Replacement phases that are supplemented with Anomalous Scattering data.  This we refer to as SIRAS, and we will use siras_phase.inp.

Run this by typing:

% cns < siras_phase.inp |tee siras_phase.log

The output will include an hkl file that contains all of the calculated phase information.  You should also carefully examine the log file.  You can now use the new hkl file as the input for solvent flattening, which will greatly improve the map.