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Command: swapna

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

The swapna command performs a virtual mutation of a nucleic acid residue by replacing its base. See also: swapaa, torsion, build, altlocs

One or more nucleic acid residues to change can be specified in a single command, and the new-type is a one-letter code representing one of the standard nucleic acid bases: A, T, G, C, or U (case is unimportant). The geometries of the new residues may not be optimal.

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 / December 2022