                      TANDEM HELICITY

    This 3D editing feature is designed to impose a  helical
structure  on  the  connecting single strands of the topmost
set  of  tandemly  connected  stems.   Defining  stem  A  as
preceding  stem  B  (and stem B succeeding stem A) if its 3'
end occurs before the 5' end of stem B, we can  then  define
stem A and stem B as being tandemly connected if there is no
stem which succeeds stem A and precedes stem B.  The topmost
set  of  tandemly  connected  stems  is then just the set of
stems which do not occur in the branching loop of any  other
stem.   How  this  set  of  stems  is  to  be  drawn  in the
representation of the 2D structure is quite  arbitrary,  but
by  convention  they  are normally arranged in the form of a
circle and thus are imagined to be in the branching loop  of
a  pseudostem  having a single 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 the contained stems because the ends  of  the
branching  loop  of  the  pseudostem  are  not  constrained.
Accordingly, there is the problem  of  how  best  to  assign
positions to the topmost set of tandemly connected stems.

    Our approach to  this  problem  is  the  simple  one  of
maximizing  the base stacking within each and at the ends of
the connecting single strands.  This amounts to winding each
connecting single strand in helical A form, using the 3' end
of its 5' connecting stem as a helical reference,  and  then
using  the  3'  end  of  the  connecting  single strand as a
helical reference for its 3' connecting stem.  The result is
a  tubular structure in which adjacent stems will be stacked
if the connecting single strand is of zero  length  (has  no
bases).   The winding procedure is invoked by activating the
'Tandem  Helicity'  item  of  the  3D  Edit  pulldown  menu.
Undesired  stem  stacking as might occur cannot be undone at
the 2D level, but it can be modified by using  the  'Segment
Position'  3D  Edit  item.   Thus,  if stem A and stem B are
tandemly connected and stem A precedes stem B, then defining
a  segment X as beginning at the 3' end of stem A and ending
at the last base of the primary sequence, segment X  can  be
rotated  about  the  3' end of stem A to give it any desired
relative orientation.

                          THE END

