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HOMOLOGOUS SEGMENT REPLACEMENT

    It is sometimes  convenient to replace the atomic coordinates of
a segment of one 3D model with those of a homologous segment of another
3D model. As an example, suppose we are working with the 3D structure
of model B and we want to take advantage of the known 3D structure of
one of its branches, say a stem-loop having an NMR-determined structure
that is part or all of a PDB file. We import the PDB file into model A,
define the segment of interest by selecting its endpoints, define the
segment of model B to be replaced by selecting its endpoints,
and then invoke the replacement algorithm.

    The term 'homologous' is here used in the strict sense that the corresponding segments have the same length and the same nucleotide
sequence. A further requirement is imposed by how the replacement
algorithm works. Assume the PDB file nucleotide sequence consists
of three parts C1, S1 and D1 such that C1-S1-D1 is the whole
sequence and  S1 is the segment of interest.  Similarly, that C2-S2-D2
is the B model sequence and S2 is the segment to be replaced by S1.
Coordinates of the S1 nucs are first defined in terms of the absolute
coordinates of it first nucelotide, and the relative coordinates of
D2 nucs are defined in terms of the absolute coordinates of the last nucleotide of S2.  The replacement is then implemented by the following
steps: (1) assign the first nucleotide of S1 the absolute coordinates
of the first nucleotide of S2; (2) using the relative coordinates of
S1, assign to S2 absolute coordinates based on the new absolute coorindates
of the first nucleotide of S1; (3) using the new absolute coordinates
of the last nucleotide of S2, assign new absolute coordinates to the
D2 segment. Segment S2 thus acquires the conformation of segment S1
and the D2 segment is moved to accommodate this change while retaining
its conformation.

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