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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.
Xplor-NIH 2024-09-13