                   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.

                          THE END

