Since the bulk solvent density is not usually known,
the solvent structure factors must be scaled to
the FCALC terms. Also, the grid being transformed has a sharp edge between
the
solvent and solvent-excluded regions, so Fourier ripples are generated that
adversely affect the high-resolution terms. A large
temperature factor can be applied to smooth these edge effects. Thus,
a DO statement,
,
is used to correct
the calculated solvent structure factors in FPART. 
and
are determined empirically by iteratively searching for the
value of one parameter that minimizes the R value in the lowest-resolution
shell without significantly increasing the high-resolution R
values, keeping
the other parameter fixed. Typically, initial values of
k=0.40 e
Å
and
B=200 Å
are chosen. The X-PLOR shell language is used to
loop over
values of k in a coarse search; the optimum value of k is subsequently
used in a coarse search to optimize B. This procedure is subsequently
repeated over
a finer set of values for k and B. All search procedures have to
be done manually.
The following example shows how to compute the solvent mask:
The next example shows how to test various scale and B-factors. Note that this protocol has to be run several times with different trial scale factors and B-factors. One should look at low R values for the low-resolution bins while maintaining low R values for the high-resolution bins. This is a somewhat subjective procedure, which is the reason why this protocol is not automated.
In subsequent protocols, one should include the following lines before computing R values, crystallographic targets, or electron density maps:
reflection @amy_s end {*Reflection file with solvent mask FPART.*}
resolution 40. 2.
do ( FPART= 0.4 * exp(-200*(s()^2)/4.)*FPART )