.fi
.ll 60
.pl 5
.ce
BACKBONE DIHEDRAL CONSTRAINTS

    Except for some sugar puckering and the 'Chi' angle determining
the orientation of the base part of a nucleotide relative to its sugar
moiety, the conformation of an RNA molecule is primarily determined
by the value of its backbone dihedral (torsion) angles. For each
internal nucleotide these are designated as:
.nf

	'alpha' about the bond P-O5'
	'beta'    "    "    "  O5'-C5'
	'gamma'   "    "    "  C5'-C4'
        'delta'   "    "    "  C4'-C3'
        'epsilon' "    "    "  C3'-O3'
	'zeta'    "    "    "  O3'-P

.fi
For a 5' nucleotide the angle 'alpha' does not apply, and for a 3'
nucleotide the angle 'zeta' does not apply.

    As an example, it is a characteristic feature of the Hammerhead
RNA molecule
that it contains the conserved segment CUGA in a conformation that
is virtually identical to that of the same segment in the yeast
phenylalanine  tRNA
anticodon loop.  We thus have what appears to be a backbone
dihedral motif.  Our preliminary attempts to predict these motifs
starting from the secondary structure of the tRNA anticodon stem
and its loop or from the secondary structure of the Hammerhead RNA,
have not been entirely successful.  For the motif to show up in 
reasonable computation time apparently requires the stabilizing 
influence of a hydrated Magnesium ion strategically placed to
interact with the CUGA segment. Preference is therefore given
to the equivalent but more practical alternative of simply
specifying dihedral constraints that will insure realization of
the motif in a refinement subsequent to generating the initial
3D model.

    Like specifying hydrogen bonding constraints, adding
backbone dihedral constraints to the current 3D model is
interactively achieved via
an item of the 3D Edit pulldown menu, called Backbone Dihedral
Constraints.  The constraints can be entered manually, as a saved list,
as a user motif or as a sample motif.  Sample motifs are those provided
with the progam.  User motifs are those provided by the user and which
are stored in the user's RNA_2D3D/Dihedral_Motifs directory.
Typical entry of a motif into this directory is by copying it from
a PDB file.  For instance, by first calling in the sample transfer
RNA file 6tna.pdb (provided in the sample PDB file directory) as
Model A, and then using the dihedral angle measuring utility (an
item of the 3D Utils pulldown menu) to
list the dihedral angles of the segment CUGA (specified by pointing
to its first and last bases), subsequent saving of this list provides
the user dihedral motif called 6tna.pdb.CUGA.

    Adding a dihedral constraint requires at least two steps. The first
is to select the desired constraint and the second is to accept it.
When the desired constraint(s) is in the form of a motif, another
step is required to indicate where in the molecule the motif is to
start.  This is achieved by specifying the corresponding motif
segment in the molecule by picking its first base in the molecule.
For instance, if the motif 6tna.pdb.CUGA is being added, picking
the base C in the molecule will tell the program where the constraints
are to be applied.

     Once a constraint has been added, and thus become a part of
the molecule's current dihedral constraint list, it can be viewed
graphically by activating the "render current list" item.  This
item toggles on and off the rendering of all the current dihedral
constraints by displaying the target angle and the current angle
of each dihedral at the midpoint of the bond about which the rotation
angle is defined.  The current angle is in parenthesis to distinguish
it from the target angle.

    Whatever the source of a specified dihedral constraints, they 
automatically will be incorporated into any subsequent refinement
procedure of the current 3D model being edited.

.ce
THE END
