Command: swapna

Usage:
swapna  residue-spec  new-type-list [ preserve  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:

• a single one-letter code representing one of the standard nucleic acid bases: A, T, G, C, or U (capitalized or not) to use for all specified residues. Examples:

  swapna /B:13 G
  swapna /A:3-5,12 T

  a list of such codes separated by commas only, with exactly as many codes as the number of specified residues; the residues will be replaced with the types according to the order in which both were specified. Example:

  swapna /A:3-5,12 A,T,G,G

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.