DENS_MOD

• RMS_FIT
• MAK_MASK
• DM_PREP
• DM_NEXT

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.html and MAIN_DOC:nmol/nmol.html) and below.

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

The menu is created with MAIN_CMDS:load_dens_mod.com.

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".

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".

DM_PREP

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".

DM_NEXT

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".