For the purposes of calculating a conventional Fourier synthesis,
both the presence and the value of *F*_{000} can safely be ignored.
The reason is, of course, that for the conventional syntheses, *F*_{000} is simply a constant term that is
added to the electron density distribution. Changing its value will only change the mean electron density and nothing
more. Given that most macromolecular crystallographers prefer to contour their maps with first contour at the mean
electron density plus something`x`rmsd,
it has become a macromolecular norm to actually prefer setting the *F*_{000} to zero, so that the
first contour of the maps is always at something`x`rmsd.

** F _{}=0 is bound to fail with the maxent maps.** Let
me illustrate this with an example. The following graphs show the distribution of density along a line containing the
origin peak of a Patterson function projection

Taking the trends apparent from these graphs to their extreme, you could argue that
as the value of *F*_{000} tends to 0.0 *e*^{-}, the peaks in the map
will tend towards functions. This line of reasoning immediately warns you that by ``adjusting'' the
value of *F*_{000}, you can make your map look as sharp as you please although your data (meaning the data that you
have indeed measured) are the same. The point is of course that *F*_{000} is NOT an adjustable quantity : the
sharpness of these maps is not required by the data that you measured, but by the value that you arbitrarily decided
to assign to the *F*_{000}. What * GraphEnt* will give you is (or, better still, I hope it is) what is required by the
data (including the assignment of *F*_{000}). If you tell the program that
*F*_{000} = 10.0 *e*^{-}, then * GraphEnt* will
give you peaks as sharp as needed for the sum of electron density on the unit cell to be 10.0 *e*^{-}. The result will
be that noise will also appear as sharp peaks, and you are bound to mis-interprete your map^{18}.

The one and only consistent way of doing the calculation is to give *F*_{000} its correct value.
This sounds very nice, but in real life things are not so straightforward : what should the *F*_{000} value be for
an isomorphous difference Patterson calculation using acentric terms (in which case even knowing
from before-hand the number of substitution sites doesn't help because
*F*_{PH} - *F*_{P} *F*_{H}) ?
what should the *F*_{000} value be for a
(2*mF*_{o} - *DF*_{c})exp(*i*)
difference map phased from an incomplete poly-alanine model ? should
the *F*_{000} include the number of electrons due to bulk solvent although I only have data from
8Å (and some strong
data are missing because they were overloaded) ? etc.
For these reasons, and in order to keep the procedure of running * GraphEnt* automatic (at least for the first time), I have
resorted to the following unjustified and arbitrary assumptions about your *F*_{000}s :

**Phased syntheses :**Assuming a that your crystals contain 50% 2M ammonium sulphate and 50% protein, their mean electron density is expected to be around 0.40*e*^{-}/Å^{3}. The assignment then is*F*_{000}= 0.40*V*_{cell}*e*^{-}, where*V*_{cell}is the volume of your unit cell in Å^{3}. I sincerely hope that for the majority of macromolecular problems this is an overstimate of the true value (which is no harm. The maps will not be as sharp as they ought to, but it will not be possible to mis-interprete them). If on the other hand, you are calculating a Fourier synthesis for the heavy atom structure (in which case the assumed*F*_{000}is much too high), you are better off stoping the calculation after the`MAXENT_AUTO.IN`file has been produced, edit it and add a reasonable definition for`F000`.**Patterson syntheses :**In this case, and because I expect most Patterson calculations to involve macromolecular isomorphous differences, I have resorted to*F*_{000}= [2*max*(*F*)]^{2}, where*max*(*F*) is the largest amplitude observed. This is a rather dubious choice which will almost certainly fail if you are calculating, for example, a native Patterson function.

** A pragmatist's view : ** If your * GraphEnt* maps
look unjustifiably sharp, increase *F*_{000}. If they look smooth, decrease
*F*_{000} till the point where you can still ``interprete'' the features that you see.

** Please note : **
The value of the *F*_{000} is only used for the calculation of the initial uniform map, but is
* not used to constrain the sum of densities in the GraphEnt maps that follow*.
In other words, do not
expect the

Quoting from Gull & Daniell, (1978),
``... Exact fitting also implies the existence of numerous separate constraints,
resulting mathematically in an unwieldy proliferation of Lagrange multipliers and
preventing calculation of the solution in all but the simplest cases''.
In the case of *F*_{000} things may not be that complex (I would think
that one additional re-scaling step
is all that is required), but given the difficulties with estimating *F*_{000} in the case
of Patterson and difference Fourier synthesis, I thought I would better leave
*F*_{000} unconstrained.

- ... projection
^{17} - This is the line
*v*= 0.5 from the example`Patt_projection.in`included with the distribution of*GraphEnt*. - ... map
^{18} - You can
actually see one of the artifacts of having too small a value of
*F*_{000}in the last two graphs. If you look carefully, you will see that it is not only the major peak that is beginning to show line splitting, but also the origin peak. The splitting of the origin peak is only indirectly due to the*F*_{000}being too small : as the peaks in the*GraphEnt*map tend towards functions, the amplitudes of the transform of the*GraphEnt*map tend to a set of normalised*E*-values with = 1 for all resulution shells. Now, because you are sampling data that go to the infinity on a finite grid (ie, the grid of your map), the power of the transform that is outside the limits of your finite grid folds back into the limits of your transform (this is usually called ``aliasing''). The most notable result is that some of the phases of the Patterson function coefficients will become*negative*, and the origin peak will start developing a hole in the middle.