                      HYDROGEN BONDING

     The specification of tertiary base pairs  in  the  base
pairing  list  of  an  RNA  molecule is one form of imposing
hydrogen bonding in addition to that  of  Watson-Crick  base
pairing  in  stems  that  is  normally  identified  with the
secondary structure.  Only the secondary structure  is  used
in  generating  the  initial  3D  structure.   Any specified
tertiary base pairing is taken into account upon  subsequent
refinement.   In the various refinement options the hydrogen
bonding corresponding to both  the  secondary  and  tertiary
base pairing is incorporated in the form of constraints.

     While  secondary  and  tertiary  base  pairing  may  be
sufficient  for some cases, there is provided the feature of
being  able  to  interactively  specify  arbitrary  hydrogen
bonding.  This is the purpose of the 'Hydrogen Bonding' item
of the pulldown 3D 'Edit' menu.   A  hydrogen  bond  can  be
typed  in  according  to a specified format which designates
the receptor and donor atoms  or  by  simply  picking  these
atoms  from  the 3D drawing.  An editable list of additional
hydrogen  bonding   can   thus   be   generated   and   will
automatically  be used in any subsequent refinement.  Such a
list becomes part of the current  Model  and  will  thus  be
saved if the Model is saved.  Alternatively, it can be saved
as    an    independent    file     in     the     directory
RNA_2D3D/Hydrogen_Bonding.

                          THE END

