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Command: swapna

swapna  residue-spec  new-type-listpreserve  true | false ] [ bfactor  value ]

The swapna command performs a virtual mutation of nucleic acid residues by simply replacing the base. The resulting structure may be poor (steric clashes, etc.). See also: swapaa, torsion, build, altlocs

One or more nucleic acid residues to change can be specified in a single command, and new-type-list can be either of the following:

The preserve option (default true) retains the existing torsion angle around the base-sugar (glycosidic) bond and the position of the base nitrogen involved in that bond.

The bfactor option allows specifying a bfactor value for the atoms of the new base; if this option is not used, the atoms will be assigned the highest bfactor value found in the residue before the swap.

UCSF Resource for Biocomputing, Visualization, and Informatics / February 2024