Sum(w*fo*fc)/Sqrt(Sum(w*fo*w*fo)*Sum(fc*fc)) {w=1 for centrics, 0.707 for acentrics, fo = |FP-FPH|, fc = fhcalc}

The advantage of this correlation is that if you include a scale factor it will cancel out. (Try it -substitute fo with s*fo and then since s is a constant (note that w and fo are not), you can move s outside the sum sign so that you have s/sqrt(s*s) which is 1). An R-factor would require a scale factor to be computed. Much of the time in refinement we don't know the scale factor yet - especially when the solution is partial. Also a least squares method would require that the scale be at least close or the matrix will be unsolvable. If phases are available from an earlier phase calculation then a phased correlation is used. In this case fc becomes |FPHcalc-FP| and w is 1 for both centric and acentric. *Note: if you want to do an unphased correlation after a phase calculation set the method to "Clear phases" and push "Apply".*. The correlation will go from 0.5 (random) to 1.0 (perfect) and takes some getting used to as it appears flat compared to other measures such as R or the correlation used in X-PLOR. A typical heavy atom will start out at 0.66 which is qute poor and refine to prehaps 0.70 which indicates a partial solution. Good solutions
are in the range 0.75-0.80 and the best ever seen is about 0.82. However these are only rules of thumb - make sure that the correlation increases with refienement and use the figure-of-merit and phasing power to track how good the derivative is.

The structure factor calculation is done with an old-fashioned summation loop using structure factor look-up tables to speed the calculations. As it turns out for solutions less than about 15 atoms this is faster than an FFT. For more on scattering factors in XtalView click here.

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. The native data should be in column 1 and the derivative in column 2 in this fin file. If you are going to use the anomalous scattering of the derivative you should use .df file. Then enter the type of phasing you want to do - usually isomorphous. For the first run select a low resolution such as 5 Ångstroms. Also its a good idea to set the outlier filter to 100-130 for weak to strong derivatives respectively. Push apply to set this data and then go back to the main window. Select the refine all derivatives method and then apply. Refinement will begin.

After you have refined then calculate some phases to check the phasing stats. (You will need to enter a phase file name at this point or the program will complain.) After you calculate some phases redo the refinement. If phases are available the refinement is sone in a phased manner. **However if the phases are poor don't do phased refinements!** Good phases will have a phasing power of 1.5 or better and a figure of merit above 0.5 for a single derivative. ** Don't forget to save your solution!**

If you have a derivative that you haven't solved you can try cross phasing it with one or more solved derivatives. Take the phases from the solved derivative and combine them with the unsolved derivative merged with the native data in a fin file. Check the swap f1 and f2 flag so that when you make an Fo-Fc map with xfft the coefficients will be FPH-FP, phimir. Positions in this map can be found with xcontur. the quickest way to find the unique peaks is to contour the entire assymetric unit by setting the bounds and slab. then pick the peaks with the mouse. The interpolated peak position will be printed out in the message window. Enter these into xpatpred and check them against the patterson map. You can add this solution to the one you already by selecting the append option on the load menu button in xheavy.

Once you have several derivatives solved and refined you are ready to phase. Increase the resolution on all the derivatives to 3 or 2.7, or whatever you have and then refine them all. At this point you can do a phase calculation and look at the stats for each derivative. Look for derivatives where the phasing power falls below 1 or so and restrict their resolution to this point. You can then rephase. If your combined figure of merit is about 0.75 or better you are probably home free at this point. ** Don't forget to save your solution!** If you are using anomalous data calculate the map in both hands. You can do this most easily by inverting all of the heavy atom x,y,z's through the origin (e.g. .1, .2, -.3 becomes -.1, -.2, .3).

Take the phases you have saved and make a map with xfft with Fo*Fc (i.e. FP*f.o.m,phimir) option and load this into xcontur. Look for the solvent channels and see if you can pick out a single molecule. If so you can take this map onto xfit. Use the solvent bounds as input in mkskel and make some ridgelines to guide you examination of the map. Load the phases into xfit and make a Fo*Fc map and load the ridgelines. Look for a helix. If you can find one check if it is right-handed. If it is then you are golden if not then you need to invert the heavy atom positions as described in the previous paragraph and rephase.

**Good Luck!**