2 BUILD_RESI_AUTO
Keyword: build, manual building
File: build_resi_auto.txt
Last: modified: 30-mar-2007

The "BUILD_RESI_AUTO" fixes distrorted geometries (returns them to
idela values) and fits fragemts of structure to electron density
considering also some energy constrainst.

Positions of atoms of the "active" selection are modified.


3 FIX_PEPT
Keyword: FIX_PEPT

Sets all peptide bonds of selected atoms to trans by fixing bond
length, angles and planarity.

3 FIT_PEPT
Keyword: FIT_PEPT

Fits peptide bonds of selected atoms to active electron density map
considering also nonbonding interactions with CB atoms and secondary
structure.

3 FLIP_PEP
Keyword: FLIP_PEP

Flips peptide bonds of selected atoms for 180 degrees. 

3 EXT_SIDE
Keyword: EXT_SIDE

Sets geometry of side chains of selected atoms to all extended (trans).

3 FIX_SIDE
Keyword: FIX_SIDE


Sets geometry of side chains of selected atoms to closes rotamer as
guessed from the dihedral angles.

3 RIG_SIDE
Keyword: RIG_SIDE

Fits fragments of residues of selected atoms to active electron
density map as rigid bodies.

3 FIT_SIDE
Keyword: FIT_SIDE

Fits geometry of side chains of selected atoms to active electron
density map considering also nonbonding interactions.

3 TRC_SIDE
Keyword: TRC_SIDE

Traces the side chains of selected residues by identifying residue
with the best fit.  It does not use any sequence information - only
the restrainst of the active density map.

TRC_SIDE finds overalps and can close disulfides.

3 FIT_AUTO
Keyword: AUTO_FIT

Combines almost all above auto fitting features as well as density
fitting under a single click.