2 DENS_MOD
Keyword: density modification, averaging, DENS_MOD
File: dens_mod.txt
Last modified: 21-jul-2007

Items of the menu block "DENS_MOD" invoke density
modifications (solvent flattening and averaging) tasks
("RMS_FIT", "MAK_MASK", "DM_PREP", "DM_NEXT").

The local macros are created via "create" scripts.  For setup explanation see
"MAIN_DOC:1mol/1mol.txt" and "MAIN_DOC:nmol/nmol.txt") and below.

For a more general scope of applications see also
"MAIN_DOC:dens_mod/dens_mod.txt".

The menu is created with "MAIN_CMDS:load_dens_mod.com".

3 RMS_FIT
Keyword: rms_fit.cmds, rms, fit, superposition, RMS_FIT

Calculates all superposition matrices among all possible pairs of
equivalent segments.  The macro calculates rotation matrices and
translation vectors, which superposition parametesr among all possible
pairs of equivalent segments and "SAVE" results to files already in a
form of a MAIN commands.  These macros are used later in density
averaging procedure to rotate the density maps.


Click invokes local macro "rms_fit.cmds".


 key ca sele atom name CA end
 rms coor all  eigen \
    sele ca .a segm name MOLA end \
    sele ca .a segm name MOLB end 
 save over file mol_MOLA_to_MOLB.com rms

Macro is configured with "create_rms_fit.pl".


3 MAK_MASK
Keyword: make_masks.cmds, molecular mask, mask, envelope, MAK_MASK

The macro checks for overlap between local and symmetry related
neighbors and when appripriate reduces the atomic radii of touching
atoms.  

A file "MAIN_DOC:nmol/make_masks.cmds" contains a list of commands
that are actually calls to "MAIN_UTILS:make_atom_mask.com" macro
providing five parameters:
- The first parameter [MOLA] is segment name of the molecule around
which a mask will be created.
- The second parameter [2] is an appropriate map from which number of
grids and layout will be calculated, usually will be used later on in
averaging,
- The third parameter is the maximal radius [3.6] of atoms applied for
mask generation.
- The fourth parameter is the map id used for the mask creation and
- the fifth is the file name into which the created mask will be
stored.

 <?MAIN_UTILS:make_atom_mask  "MOLA" 2 3.6 3 mask_MOLA.xmap

Macro is configured with "create_make_mask.pl".
 
3 DM_PREP
Keyword: DM_PREP, density modification initial map, prepare

Generates the first map of electron density and copies it into map
number 2, which serves as input for density modification procedures.

For example see "MAIN_DOC:nmol/dm_prep.cmds".

Macro is configured with "create_dm_prep.pl".

3 DM_NEXT
Keyword: DM_NEXT, density modification, cyclic averaging, averaging

Performs cycle(s) of density modification procedure as specified.

A call to a complete averaging cycle (loop) follows.  There are four
numbers. 

For example see "MAIN_DOC:nmol/dm_next.cmds" and related macros.

The click invokes TWO macros configured separately "create_dm_next.pl"
and "create_dm_loop.pl".