Example: a viral RNA helix

In cucumber green mottle mosaic virus, a single stranded RNA forms a right handed helix which is protected by the protein coats. In each subunit, one protein coat binds three consecutive nucleotides. The linkage between nucleotides in neighboring subunits has to be defined in order to preserve the continuity of the RNA molecule during the structure refinement. In the following example, a covalent bond is defined between O3$'$ of nucleotide 165 of origin subunit and P of nucleotide 167 of a neighboring subunit, which is related to the origin subunit by helical symmetry relation 2. Furthermore, the angles and dihedral angles associated with the bond are defined. The invalid non-bonded interactions including 1-2, 1-3 and 1-4 interactions are excluded.

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