.fi
.ll 60
.pl 5
.ce
SINGLE STRAND HELICITY

    In the 2D representation of a secondary structure we have adopted
the often used convention that the set of stems which are not in the
branching loop of any other stem are nevertheless drawn as though they
are in the branching loop of an imaginary stem having but one basepair.
In contrast to the case of  the branching loop of a real stem, this 2D
representation need not approximate the actual 3D disposition of
these stems because the ends of the branching loop of the pseudostem
are not constrained.  Accordingly, there is the problem of how best to
assign 3D positions to this set of stems.

    Short of doing a complete global refinement, there is no total
solution to this problem. But using the fact that single strands tend
to adopt the helical A form and that successive pseudoknots appear
to be coaxially arranged, it seems appropriate to impose a helical
structure on the two free ends and on the single strands connecting
pseudoknots.  This is done automatically in going from the 2D to the
3D representation.

.ce
THE END
