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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.

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THE END
