At the very beginning of the calculation (especially of a Patterson function), the
* GraphEnt* map may show a great deal of peaks, which later on disappear giving a map
with essentially only the origin peak. Then new features start to emerge slowly,
which more
often than not, remain till the end of the calculation. * This is an artifact
of how the program contours the section that is plotted in the graphics window* :
* GraphEnt* will always plot with the first (dashed) contour at the mean, and then every 0.5 rmsd
* of the given map section* (and not of the whole map). At the very beginning of
the calculation, the * GraphEnt* map is almost uniform, but because the program contours the plot
from the mean and every 0.5 rmsd (however small this may be compared with the mean),
the graphics window will show peaks (which in reality are just slight modulations of
an otherwise uniform map). As the calculation progresses the major features start appearing
(which in the case of Patterson functions is the origin peak), and then as the data are being
fitted more closely the finer detail starts building up. I will illustrate these
events with a series of intermediate * GraphEnt* maps produced during the calculation
of a difference Patterson
projection. To show clearly the significance of the mean density, these graphs only show
the density along a Harker line (*v* = 0.5). The data used for this example have been
discussed in section 8.1 :