3. Electron density modifications

Electron density can be manipulated by any mean that will yield a more
interpretable electron density map, leading towards a completly
resolved 3-dimensional structure.

Most of the functions described here are made available via
"main_config" utilities.  Look below only if some extra "MAIN"
programing is required and is not covered by in
"MAIN_DOC:1mol/1mol.txt" and "MAIN_DOC:nmol/nmol.txt".

USUALLY YOU DO NOT READ BELOW.

MAIN offers a map manipulation language, which allows you to do much
more as can be possibly described here.  If you want to master more
than the usual essentials, you are advised to read the "MAKE MAP"
commands from the "Reference manual".

Section "Solvent flattening" describes how to run the standard reals
space procedure (Wang, ) and the fast one, which uses the Parseval's
correlation theorem to calculate the molecular envelope in reciprocal
space.  Section "Electron density averaging" brings you essentialls of
how to setup an electron density averaging procedure. Two procedures
in two subsections are described.  Subsection "Averaging of electron
density: 2 molecules" explains a procedure within a single unit cell
and is easy expandable to any number of equivelent density regions.
Subsection "Averaging density between 2 different crystal forms"
explains how to average electron density of two equal molecules in two
different crystal forms.  Section "Electron density combination"
explains how and why combine different origin electron density maps in
order to construct better maps.  Its extension partial model
refinement is described in chapter "Crystallographic refinement" in
section "Partial model refinement".

Besides these there are some auxiliary sections, which help you to
deal with certain concepts and tools connected with MAIN map
manipulations.  Section "Making envelopes" shows how envelopes can be
constructed with MAIN.  Section "Local histogram matching" introduces
s short reciprocal space based histogram correlation procedure, which
can be built in into any kind of map calculation.  Section "Map
concepts" gives insight into map structure and map manipulation
command language.  Section "Phase combination" describes how to
combine phase combination into an electron density modification
procedure using CCP4 package.