                      COMPACTING

    This is a procedure  designed  to  give  an  initial  3D
structuring  to the single strands.  The double strands of a
3D structure occur as  parts  of  an  A-type  helical  form.
Their  structure is therefore nicely predetermined.  But how
the preformed helices are disposed in space relative to  one
another  depends  on  the structuring of the interconnecting
single strands and on tertiary interactions.

    The  compacting  procedure   is   based   on   the
hypothesis  that  single  strands  tend  to  have  a helical
structure resulting from the tendency of adjacent  bases  to
stack as they do in double-stranded helices.  Hence the idea
of simply extending the  structure  of  the  double-stranded
helices  (stems)  into the adjacent single strands by adding
imaginary (pseudo) base pairs and thus reduce  the  size  of
the single strands.

    Invoked  by  default,  the  compacting   procedure
becomes  part  of  the  process  of  forming  the initial 2D
template that is used to obtain the  initial  3D  structure.
Subsequently,  it can be interactively nullifed or modified.
Modification is done  with  the  2D  basepair  editor  which
handles   both   real  and  pseudo  basepairs.   The  pseudo
basepairs are drawn as dashed lines in the rendering of both
the 2D and 3D models.

    As  to  the  algorithm  governing  the  recruitment   of
unpaired   bases  into  the  pseudo-paired  form,  we  first
distinguish between those lying in bulges or inner loops and
those  lying  in bifurcation (branching) loops.  With regard
to the first type in which a stem consists of more than  one
region   (a  set  of  contiguous  base  pairs)  successively
separated by bulges or inner loops,  a  region  is  extended
upwards  as much as possible so that what is left between it
and the next region ( measured toward the top of  the  stem)
is  at  most  a  bulge and the two regions are then stacked.
All the regions of a stem are thus coaxially aligned.

    The  algorithm  for  branching  loops  is  a  bit   more
complicated   because   of  the  many  more  ways  in  which
extensions can be  done.   The  goal  is  to  leave  as  few
unpaired bases as possible.  A dynamic programming algorithm
is therefore used subject to the restriction that the  first
maximal  extension  found  is  the  one that is subsequently
kept.

     It is useful to keep in mind that compacting  can
change  the  size  of the secondary structure stems, but not
their relative interconnection.  What is changed, as in stem
stacking,  is  the  relative positioning of the stems in 3D,
and it is these changes which can be explored by editing the
resulting compacting with the basepair editor.

    Also to be noted is that the compacting algorithms
were  originally  conceived  for  handling strictly orthodox
secondary structures, that is, those structures which do not
contain   pseudoknots.   The   compacting   procedure  is
currently only partially applied to the  loops  (hairpin  or
branching)  of  the stems comprising a pseudoknot.  In these
cases compacting amounts to extending the helicity  of
the  tops  of the comprising stems so that the single strand
emanating from each is favorably placed in the groove (major
or  minor) of the other in order to promote potential triple
base pairing.

                          THE END


