                        PSEUDOKNOTS

    As noted in the  help  topic  STEM/REGION_STACKING,  two
stems  can  form a pseudoknot when  a strand of each is part
of the hairpin or branching loop of the other stem in such a
manner  that one stem can be regarded as a coaxial extension
of the other by stacking their tops together.  Such stacking
results in increased conformation stability.

    The pseudoknot motif is interesting not only as a  means
of  increasing  conformation stability, but also in the fact
that it can lead to a variety  of  base-pairing  topologies,
the two principal cases of which result from two pseudoknots
occuring in tandem or of one being nested within the  other.
The  RNA_2D3D  program  is  designed to handle all the known
cases.  But  because  of  the  complexity  of  some  of  the
topologies,  there  is usually required some careful editing
and post refinement to obtain satisfactory structures.

    Samples of pseudoknots exemplifying  actual and imagined
structures  are  provided in the "sample BPL" data base.  As
will  be  noticed  in  looking  at  any  of   these   sample
structures,  the stems forming a pseudoknot are colored: one
red and the other yelllow.  This  coloring  is  for  readily
distinguishing   a   pseudoknot  from  stems  which  do  not
participate in pseudoknot formation.  The stem  colored  red
is at the 5' end of the knot and the yellow at the 3' end.

                          THE END

