These commands are used to setup, modify and process the internal coordinates of the molecule. This operation is very useful in setting up atom coordinates whenever they are not known. This occurs when a protein structure is built from scratch or when an existing structure is modified. The modification can simply be a conformational change, or a change in the residue sequence through replacement,insertion, or deletion. Many of these modifications can be processed within the program as it currently stands. Other more difficult modifications can be facilitated by editing the internal coordinate file by using external programs.
The Internal Coordinate commands (except SETUP and EDIT)
can only be used if internal coordinates exist (i.e.
IC common is filled). This can only be filled
by reading an
IC file from disk, or by using the
SETUP subcommand. The use of SETUP assumes that the
residue sequence has already been generated.
The information used to setup is obtained from the
current residue topology file.
If you change to a different residue topology file,
you must do a IC SETUP before reading in the new
topology file. Otherwise, you'll be reading internal
coordinate information from the wrong place.
The subcommands are interpreted as follows:
DISTance atom atom real ANGLE atom atom atom real DIHEdral atom atom [*]atom atom real END atom::=residue_number atom_type
The first three commands will specify a particular
internal coordinate value. The DIST and ANGLE commands
require that such an IC already exists and will be
modified only. The DIHE command will search for desired
IC, and if it is not found a new set will be added
(including the associated distances and angles). In either case
the torsion angle value in the internal coordinate will be set to
the value specified.
The DELTA option specifies that the current torsion angle in the
internal coordinates be added to the specified real number to make the new
torsion angle. If the dihedral angle specified in the DIHEDRAL command
is not found in the internal coordinates, then DELTA option has no effect.
optional * on the third atom denotes that this is the
central atom of an improper dihedral angle (i.e. the
angle is determined by planes 1-3-2 and 4-3-2, also the
associated angles use the same pattern for this type).
The END command is used to exit from the edit IC mode.