2 REFINE
Keyword: refinement, positional, B-factor
File: refine.txt
Last modified: 16-jan-2003

3 KICK_ALL
Keyword: KICK_ALL, kick atoms

KICK_ALL displaces all "WORK_SEGM" atoms up to the current "KICK_VAL"
shift.

3 REFINE
Keyword: REFINE, refinement, positional, refine.cmds

Refines positions of your model using macro "refine.cmds".  Use main
config tool "menu_refine.sh" to configure the macro.

Subroutine arguments: 
- integer map number of a unit cell map (MAP_WORK) and
- character variable or string(s) of segment names used for
structure factor calculations.

For more see "MAIN_DOC:refine/refine.txt".

3 REFINE_B
Keyword: REFINE_B, b-factor, refinement, overall, individual, refine_b.cmds

Refines B-values of a model (individual and overall) against
the chosen target function using macro "refine_b.cmds".
Refines positions of your model using macro "refine_b.cmds".  Use main
config tool "menu_refine_b.sh" to configure the macro.

Subroutine arguments: 
- integer map number of a unit cell map (MAP_WORK) and
- character variable or string(s) of segment names used for
structure factor calculations.

For more see "MAIN_DOC:refine/refine.txt".

3 GEN_SOLVENT
Keyword: GEN_SOLVENT, solvent, generate

Generates new solvent molecules on the basis of peaks in a
difference density map, checks their consistency within 
an 2Fo-Fc map, their distance to hydrogen bond donors and
overlap with already existing atoms and symmetry overlap.

The newly created solvent molecule (H2O) obtain segment name
WAT2.  HINT: Modify your RE_IMAGE command to see the newly
created solvents in a different color.

The macro invoked by default is the file "MAIN_CMDS:gen_solvent.cmds",
which calls "MAIN_UTILS:gen_solvent.com", created by
"menu_gen_solv.sh" script.

Subroutine "gen_solvent.com" arguments: 
- integer map number of a 2fo-fc unit cell map (MAP_2FOFC),
- integer map number of a fo-fc unit cell map (MAP_FOFC),
- character variable or string(s) of segment names around
which new solvents will be added,
- character variable or string(s) of segment names around
which new solvents will be added, which do not include any
solvent molecule in order to enable control of solvent
layers added.