2 MODELER
File: >doc/menu/modeler.txt
Last modified: 13-apr-2019

The modeling functions ("RT_CHAIN", "MOV_ATOM", "MOV_RESI",
"MOV_SELE") activate OBJECTS for interactive spatial modifications of
molecular geometry and assign DIALS to them.  After the geometry has
been changed using mouse or dials, the change has to be accepted using
"OBJ_ACCE" or rejected "OBJ_REJE".

Remember first to pick the atoms and afterwards pick an ITEM.  The
last picked atoms may be used any number of times.

All these commands can be applied in any combination on various or the
same group of atoms. The order in which they are applied does matter -
eroneous combinations may result in eroneous results (first defien
bodn rotation and the a rigid body bovement of the moving atoms by
"MOV_RESI" or "MOV_SELE".

(See also DIAL_SAV and DIAL_RST regarding DIAL set storage end
retrivial.)

See also "MAIN_MENU:history.txt" and "MAIN_MENU:nice_sel.txt".

3 MOV_SELE
Keyword: MOV_SELE, rotate and translate

Does rigid body movement (combines "ROTATION" and "TRANSLATION") of
the selected atoms (key "active") using the last PICKED atom as the
center of rotation.  The simplest way of selecting atoms is using the
functions of the menu block "nice_sel.txt".  Shortcut is "x".

3 MOV_RESI
Keyword: MOV_RESI, move residue

Does rigid body movement (ROTATES and TRANSLATES) of the residue
disregarding the connectivities of that particular residue.
(You don't have to break bonds as in the case of the "ROT_TRAN"
command.)  The center of rotation is the last picked atom.

3 MOV_ATOM
Keyword: MOV_ATOM

TRANSLATES the last PICKED atom disregarding its
connectivities.  (You don't have to break bonds as in the case
of the TRANSLAT command.)

Does not save the DIAL set automatically.

3 RT_CHAIN
Keyword: RT_CHAIN, rotate chain, rotate, conformation, dihedral

RT_CHAIN activates rotation of all BONDS between the last 2
PICKED atoms.  MAIN is only capable of checking each separate
bond rotation.  When there are more bonds to be rotated in the
chain and one is a part of a ring, an error message will
appear.  In such case you should hit "OB_REJECT" and pick a
different pair of atoms.

The menu item "RT_CHAIN" calls within a loop a variety of command
files, one for each rotatable bond. After each 8th bond, the
DIAL WRITE sentence is automatically done.  

3 Acive objects
Keyword: OB_START, OB_REJECT, OB_ACCEPT

OB_START
> OBJECT int SET INIT

OB_REJEC
> OBJECT int SET TRUE

OB_ACCEP
> OBJECT int SET FALSE

These commands affect all activated OBJECTS. The objects are either
returned to their initial position ("OB_START"), rejected (OB_REJEC)
or accepted ("OB_ACCEP").  Only "OB_ACCEPT" changes atom coordinates.
After "OB_REJEC" and "OB_ACCEP" the complete image is redrawn.