2 MAP_ATOM
File: map_atom.txt
Last modified: 30-mar-95

MAP_ATOMS together with the MAP_IMAGE blocks enable you to
interactively create and modify electron density maps with
using molecular models (ATOMS) under visual control.
(MAP_ACT? items of both blocks are identical - they both
reffer to the same variable.)

Active map density can be modified in the radius (ATO_RAD?)
around 'active' atoms.  Density values can be either set to
mask (ATO_MASK), empty (ATO_CLEA) or atom density values
(ATO_DENS).

The ATO_DIFF creates a difference electron density map,
where the generated density from the 'active' key atoms is
subtracted from the active map.

The commands RE_PHASE, 2FO-FC_M, FO-FC_MA, REFINE,
SKELTONIZE, MASK_FLAT, SOLV_FLAT govern structure factor and
map calculations, crystallographics refinement and map
skeletonization and two solvent flattening approaches.


3 MAP_PAS?

3 MAP_ACT?

3 ATO_RAD

> menu block MAPS_EDIT item ATO_RAD? add text "<>cmds/make_map_radius.cmds"

3 ATO_MASK

> menu block MAPS_EDIT item ATO_MASK add text -
>  "make map map_to atom mask map_rad select active end"

3 ATO_CLEA

> menu block MAPS_EDIT item ATO_CLEA add text -
>  "make map map_to atom clea map_rad select active end"

3 ATO_DENS

> menu block MAPS_EDIT item ATO_DENS add text -
>   "make map map_to atom dens select active end"

3 ATO_DIFF

> menu block MAPS_EDIT item ATO_DIFF add \
>       text "<>cmds/make_map_atom_diff.cmds"

3 RE_PHASE

Calucaulates structure factors (PHASES) and R-factor of your
current model.  You should always use your own files. The
file ">cmds/re_phase.cmds" is only an example that
should be adjusted to almost each particular case.


3 2FO-FC_MAP

Calucaulates an 2Fobs-Fcalc map on the basis from the last
calculated structure factors. You should always use your own
files. The file ">cmds/calc_2fofc_map.cmds" is only an
example that should be adjusted to almost each particular
case.

3 FO-FC_MAP

Calucaulates an Fobs-Fcalc map on the basis from the last
calculated structure factors. You should always use your own
files. The file "main/cmds/calc_fofc_map.cmds" is only an
example that should be adjusted to almost each particular
case.

3 REFINE

Refines your model against a Fobs-Fcalc map.  Structure
factor update step numb can be specifed.  

The file "main/cmds/refine.cmds" is only an example that
should be adjusted to almost each particular case.

3 SKELETONIZE

Skeletonizes a map.  You should specify the density cutoff
level and size of segments that should be drawn on the
screen.  The skeleton atoms are accessible through the key
"skel".

The file "main/cmds/get_skel.cmds" is only an example that
should be adjusted to almost each particular case.

3 MASK_FLAT

Calculates structure factors of a solvent flattened map.
Envelope is created from an atom selection.  You can use
your model or skeleton atoms or whatever kind of atoms
you may have.

The file "main/cmds/mask_flat.cmds" is only an example that
should be adjusted to almost each particular case.

3 SOLV_FLAT

Calculates structure factors of a solvent flattened map.
Envelope is created by the standard Wang sphere statistics
procedure.  Try to limit the procedure to a asymetric unit
and later generate the whole unit cell from it. The
procedure takes some time.

The file "main/cmds/solv_flat.cmds" is only an example that
should be adjusted to almost each particular case.