Addgrp adds a new chemical group whose position is determined by the three specified atoms. The parameters required are the group name (which corresponds to a file in a directory, see below), the bond_length from atom1 to the first atom of the added group, and the bond_angle formed by the group being added, atom1 and atom2. Dihedral_angle (formed by the added group, atom1, atom2, and atom3) must be a positive value between 0 and 360, inclusive. It defaults to 0. New_residue_name defaults to the old residue name.
Group files are searched for in $HOME/groups/ [user's groups] and /usr/local/midas/resource/midas/groups/ [system groups], in that order. The user should check the system groups directory to determine if a description of the group he/she wishes to add exists, and if so what the file name is. If there is no system file for the group, the user may create one and place it in his/her personal groups directory. The easiest way to create a group file is to use the pdb2group utility provided that the user has a PDB file containing the chemical group. Otherwise, the group description will have to be created by hand. See the format description in the pdb2group manual page.
Note that adding a group creates a new residue which is colored white and has no labels. The temperature factor for the new residue is set to the highest currently found in the model.
The user's groups directory location can be overridden by setting the GROUPS environment variable to a directory or a colon-separated list of directories. If the GROUPS environment variable is not set, and $HOME/groups/ does not exist, then the current directory will be searched instead.
See also: delete, Build Structure