2 MINIMIZE
File: minimize.txt
Last modified: 28-sept-1994

Atoms SELECTED in KEY "active" are MINIMIZED against
background of "passive" KEY atoms with the ENERGY terms turned
ON.  'active' atoms are allowed to move and 'passive' atoms
are there only to interact with 'active' atoms.  The key
'passive' should include all 'active' atoms, otherwise
'active' atoms will not be treated properly.

When applying PAIR constraints take care that anchor do not
become a part of the 'active' key.  Anchors do not need to be
included to the 'passive' key.

MINI_ANH minimizes anchors in an electron density map
gradients.  I recommand you to use this option a lot.

See for example the
">utils/def_top_par_19.com" file, which is the default macro invoked
through the "DEFINE" item.  You can redirect these calls
by redifining the variable DEF_ALL.  Try

> show vari DEF_ALL 

to check the variable status.

> defin clas charge by topo
> defin bond angle by auto
> defin dihe improper by topo

DENSITY energy term is a negative correlation of a "real" atom with
the density of the chosen map.  For comfort model building see also
the below session "Use of anchors" and the session "Load_xray_maps" in
the part "Dialog mode accessories".

> ener density map 1 density scale 30.