7.4. Generating molecular envelopes

Molecular envelope or a mask is a region within a map, which is
accounted to one or several molecules.  Points of a molecular mask in
the real*4 map presentations have values larger than 9998.0.

Masks can be created with help of atoms by masking all grid points within
a ceratin radii from the selected atoms and write it to a file.

> make map MAP_MASK from 1 init -9999 around 10 select segm name A end
> make map MAP_MASK select segm name A end atom mask 4.0
> write fils model_mask.xmap map MAP_MASK xplor

In the simplest case a molecule is already available, so we can simply
used it for the mask.  In cases when this is not, a mask should be
created out of a given electron density map.  As soon as the electron
density electron density interpretation proceeds, include the current
models in mask editing procedures.

7.4.1.  Filling holes and removing lonely clouds

Remove cloudes, which have less than a HOLE_SIZE in diameter, from a mask:

> make map MAP_MASK + 1 from MAP_MASK init 9999 copy
> make map MAP_MASK from MAP_MASK + 1 remove HOLE_SIZE

Enlarge the mask for the holes which have less than HOLE_SIZE in
diameter.

> make map MAP_MASK + 1 from MAP_MASK init 9999 copy
> make map MAP_MASK from MAP_MASK + 1 fill HOLE_SIZE

7.4.2. Avoiding mask overlap(s) in a unit cell

Since the masks are based on atoms, the simplest is to check the
symmetry overlap interactively on the screen by adapting a
"re_image.cmds" and "symmetry.cmds" files so that they will generate
images of the atoms used for a mask generation and their symmetry
equivalents.  Fiddle with the atoms until no overlap is seen (display
maps and use them for defining an asymmetric unit when they are
available).

The mask atoms in contact their symmatry mates need a reduce radius.
The simplest way, however, is, to generate the symmetry mates around
the masked atoms and then used them to remove the regions, they
occupy, from a mask.  Of course their radii should be reduced when
compared to the radii used for the mask creation.

> delete atom sele segm name #* end
> symmetry select mask_atoms end around select mask_atoms end dist 10. cut
> make map MASK_MAP atom clear 1.8 sele segm name #* end

You can inspect the mask overlap also by using the masks
to generate the unit cell.

7.4.3. Using secondary structure elements (helices)

A polypeptide chain folded into a secondary structure (a helix) can be
used to efficiently mask substantial regions of space.  With this
models it is easy to check possible overlaps with a symmetry related
regions.  It is enough to master the elementary model building
features and the way to ab initio envelope creation is open.  The
disadvantage of maps based on secondary structure models is that such
models only approximately follow a map.

7.4.3. Exploiting map skeletons

Skeleton is a way of an electron density map presentation, where
skeleton atoms are conected with covalent bonds and displayed.  The
implemented algorithm is based on S. Swansons ideas.  Skeleton atoms
are placed at local density maxima and on saddle points connecting
them.  The maxima as well the saddle points have to be above a chosen
density threshold level. See "MAIN_MENU:map_mask.txt" for further
instructions.

It remains to select the molecular regions.  The easiest way to
prepare masks is by using the SELECT menu block items and when needed
to break connection and delete one or several atoms.  For this
purpose the key 'active' is exploited.

Use only the default flags of the SELECT (light blue) menu block.
Items 'KEY_ACTI', 'SEL_LAST', 'SELE_nn ' and 'SEL_MOLE' should be
activated.  With this flags on, you will choose only whole networks of
covalent bonds (molecules).  By picking atoms and functions 'SEL
.or.', 'SEL.and.' and 'SEL.not.'  enable you to select whole segments
with help of logical operations: with 'SEL .or.' you include into the
key 'active' additional network of skeleton atoms, with 'SEL.and.' you
keep only the last picked network and with 'SEL.not.' you exclude the
last network from the key.  If a network is too large you can break it
into smaller pieces by breaking bonds ('DELE_BON') or deleting some of
its atoms ('DELE_ATO').

After the process is finished you can write the selected atoms to a file
or immediately create a mask.

7.4.6. Procedures based on map statistics

The simplest approach is mask definition during a solvent flattening
cycle.

7.4.7. Placing atoms on a 10 grid lattice