Notes on using phases calculated from one lousy heavy atom derivative
to locate the sites in a second derivative,  and then use both derivates
together to calculate an interpretable electron density map (using CNS):

The goal of this example is to use L9 Hg derivative data (file = thim.cns)
to calculate a pretty lousy "one-derivative map" and initial phases for the
L9 native data (filename = e100c_nat3.cns). These phases are then used to
to calculate a difference fourier map of the L9 iodine derivative
(filename = e100c3i.cns).  This difference fourier map contains large
peaks at the iodine sites.  Thus, the iodine sites can be found without
having to solve a Patterson map.

Note that the large iodine peaks in the difference fourier map are negative;
this is because the input file is set up to calculate the difference fourier
map as "native minus iodine".

To see negative peaks using "O", just set the map contour level to a negative
number in the "map_parameter" line.

In addition to the 2 iodine peaks, the difference fourier map contains a
third large peak at the Hg site; this 3rd peak is an artifact.

Note that these map calulations do not require a structural model or PDB file. However,
a PDB file for L9 is included in this directory (l9.pdb) so the sites can be seen
relative to the L9 structure. The Hg site is near the side chain of residue
E100.  The two iodine sites are near the ring of tyrosine Y126. The two iodine peaks
are not the same height, but they are both present.

Input files:  All these files are on hermione in  /home/dave/cns_examples/L9_2deriv/ 
The files can be copied into your directory and run.

e100c_nat3.cns = L9 native data

thim.cns = Hg derivative data (thim = "thimerosol", an organic Hg compound)

e100c3i.cns = iodine derivative data

merge.inp => merges native and thimerosol data sets

scale.inp => scales native and thimerosol data sets

ir_phase.inp => calculates phases for native data using thimerosol derivative

fourier_map_mir.inp => calculates electron density map for L9 based on phases
                       from the thimerosol derivative only.  Note that the
                       map is not interpretable.

fourier_map_mir_2.inp => calculates difference fourier map for iodine derivative
                         using phases from thimerosol derivative. The map is calculated
                         as "native minus iodine", so the iodine peaks are negative.

Now that the iodine sites are found, the iodine sites can be used together with the
Hg site to calculate an electron density map that is actually interpretable.