14.2 Purpose of the Various Internal Coordinate Commands

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. if the 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:

SETUP

Setup the internal coordinates using standard values from the parameter file, unless otherwise specified in the residue topology file (see RTF File Formats). The internal coordinates are built from the current RTF.

FILL

Fill the internal coordinate values wherever possible from the known atomic coordinates. No changes are made to internal coordinates which have atoms that have unknown positions. If the COMP keyword is used, then the alternate coordinate set will be used to fill the IC data structure.

EDIT

Edit the internal coordinate file. This command causes the input stream to transfer to the IC edit mode. The edit mode commands are:

          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. The 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.

BILD

This command determines the cartesian coordinates for all unspecified atoms from the data in the IC file (wherever possible). The user is responsible to make sure that the designation for all atoms is unique. In the case that the system is over specified, An atom is placed on the first opportunity. If it is desired to modify the position of atoms with known coordinates, the coordinates for those atoms must be reinitialized using the COOR INIT command. Again, if the COMP keyword is used, then the alternate coordinate set will be used and modified.

SEED

When the cartesian coordinates are not specified for any atoms, the BILD command cannot be used to generate positions since all positions are determined relative to known positions. The SEED command specifies the positions of the three atoms . It puts the first at the origin, the second on the X-axis, and the third in the XY-plane. The three atoms must have entries in the IC file of (dist 1-2, angle 1-2-3, dist 2-3). The COMP keyword causes the alternate coordinate set to be used.

DELETE

This commands deletes a specified set of IC's from the data file. The delete can be by number (using the BYNUM keyword and a range), or by atoms selection. Any IC that contains a selected atom will be removed.

KEEP

The keep command is the logical opposite of the DELETE command. Its options are identical, except that the selected set of IC's is kept, and the remaining ones are deleted.

PURGE

This command causes all partially specified IC's to be deleted. Only the IC's with all four atoms defined will be kept. The IC's that remain will be renumbered.