After phases are available scaling is straightforward as the value of FPHcalc-FP can be directly computed. After scaling another problematical area is the estimate of E, the error in fh due to all causes. If this value is underestimated then the phases will be given too much weight as the ditributions will be too small and if E is too large the phasing power will be underestimated. The exact equation for E is given as equation 3.17 in my book Practical Protein Crystallography . The phases are saved either in the form h,k,l,FP,f.o.m.,phi or h,k,l,FP,f.o.m.,phi,A,B,C,D depending on the method chosen.
Strategies Use xpatpred to start the first solution file.
In xpatpred you can enter in heavy atom positions and then compare these with the patterson map. Save the predictions from xpatpred in a file and then load this file into xcontur as a label file while displaying the map. Once you have a solution that explains the peaks in the patterson map then save the solution file in xpatpred and read it into xheavy. Click on the derivative in the derivative list and then select Edit. You will need to enter the fin file that contains the heavy atom data merged with the native data.