Menu itesm in "MAP_MASK" help you to recognize and select the asymmetric unit for either further density modifications (solvent falttening and averaging) or model building.
The menu block "MAP_MASK" is loaded with macro "MAIN_CMDS"load_map_mask.com"to page No. 10"to page No. 10.
This is a pre-step for density modification procedures. Creates score map which serves as the basis for differentiation of solvent and macromolecule regions.
The analysis shows (SHOW ANAL) which density score level approximately separates molecular from solvent region. You are advised to display the score map and carefully inspect it at different contouring levels and then decide about your solvent content and cutoffs.
The macro MAIN_CMDS:map_mask_score_map.cmds is only an example that should be adjusted to almost each particular case. The procedure calls MAIN_UTILS:solvent_mask_solomon.com, which you may also wish to edit.
Skeletonizes a map. The macro finds extrems and connects them through saddle points. Extreme and saddle points are converted to atoms and connections to covalent bonds between them.
It is assumed that the MAP_2FOFC, or MAP_FO (both variables) point to the map number 1, which is by default a unit cell map that will be skeletonized. In order to change the box in which skeletonization is performed copy the MAIN_CMDS:map_mask_skel_gen.cmds macro to your working directory and tailor it to your needs.
If it happens that you run out of memory limits, choose a larger MAIN version or skeletonize only a portion of a map.
See also the chapter "Molecular replacement" (MAIN:doc/mol_repl/mol_repl.html).
Displays image of "skeleton" atoms in two colors. The skeleton atoms selected in the key "active" are shown in different color.
The default macro is MAIN_CMDS:map_mask_skel_ima.cmds.
Displays image of the symmetry equivalents of the "active" skeleton atoms. Used to verify overlap of the "active" atoms with its surroundings during a search for asymetric unit.
The default macro is "< ?MAIN_CMDS:map_mask_skel_sym.cmds".