Click on a secondary structure item sets conformation of "active" protein main chain atoms to standard helices, beta sheets or other regular patterns. Conformation conversion starts rotating 'active' atoms around predefined bonds from N-(FORWARD) or C-(BACKWARD) terminus, depending whether "FORWARD" or "BACKWARD" flag is set.
Click the "DIHEDRAL" item requires preceding atom picking and a dihedral value from the keyboard. DIHEDRAL is not limited to some standard atom types and dihedral angle value(s). You can define any dihedral angle among any four atoms you want.
Clicking standard (1-4 BETA, 1-3 GAMMA) turns items changes conformation of the second and third residue FORWARD or BACKWARD from the last picked residue by 1-4 turns while by 1-3 turn only the second residue conformation is changed.
All geometry changes are instantaneous, no confirmation is required. "UN_DO" can get you one step backwards. In the case you have messed up everything, you have to extract the last editing session commands from the created "input.cop" file and insert a return command before the command where the mess begun.
The menu is encoded in MAIN source, so can not be changed.
For command syntax see MAIN_COM:secondary.html.
The "SECONDARY" structure elements MENU is placed on the page 8 and shown in violet.
Secondary structure elements can be applied in block ("HEL_ALPH", "HEL_3-10", "COLLAGEN", "POLI_PRO", "BET_ANTI", "BET_PARA", "EXTENDED") by acting on the "active" selection or as turns ("TURN_I", "TURN_II", "TURN_III" and their "primes"', "GAMMA" and "GAMM_IN"-verse turns) acting on the next four or three residues away from the last clicked atom.
The model changes conformation "FORWARDS" or "BACKWARDS" from its N-terminus towards C-terminus of a chain or vice versa. Its starting terminus preserves the position.