File: refine.txt
Last modified: 16-jan-2003

REFINE

KICK_ALL

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

REFINE

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

Subroutine arguments:

For more see MAIN_DOC:refine/refine.html.

REFINE_B

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:

For more see MAIN_DOC:refine/refine.html.

GEN_SOLVENT

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: