baton_mode [option]
This command controls the orientation and position of the di-peptide when Baton_build is active. If the mode setting is alpha, the coordinates of the last 4 CA atoms are taken and a least squares comparison made with a regular alpha-helix. The di-peptide is then placed in the position of the 4th and 5th residues of the helix. If the mode is beta, the comparison is made with residues from a regular beta-strand. If the mode is 2ry, a comparison is made with both alpha and beta structures, and the one closest to the last 4 residues is used to position the di-peptide. In all three modes, if 4 residues have not been built, the mode defaults to a `standard' orientation for the peptide. This can also be achieved by defining mode ? or any other non-recognized character string.
The option may also be the name of a skeleton molecule. The program uses the current connectivity of this molecule to place one end of the di-peptide on a line joining 2 bones atoms, if these atoms exist. If more than one pair of atoms exists, the program creates a list of suggestions. Multiple calls to this command cause the peptide to be placed at different positions within this list. The order of items in the list is determined by the bones status of the pair of skeleton atoms; pairs of class 1 atoms first, followed by pairs of non-class 2, followed by mixed 2/other etc., and by the direction of building. This option, therefore, makes it easy to follow a skeleton or to build standard secondary structure elements, or anything in-between.