The Refi Dictionary

The dictionary used by O and FRODO is described by Hermans & Ferro in Biopolymers, Vol. 10, pages 1121-1138. The connectivity is represented as a tree structure of backward and forward pointers. Bond lengths and angles are defined via the back pointers. The full dictionary of Jan Hermans also has the possibility of defining non-bonded atom energy coefficients. The first record is a title The next record defines the residue type and the number of atoms in the dictionary description of the residue. The format is (A4,6X,I5). A residue name END terminates the file. Each atom has one record defining the name, back chain, lowest forward chain, highest forward chain,a flag to define fixed or flexible torsion angle,a bond length, a bond angle, a torsion angle. The format is (A4,2X,4I2,3F5.0).

The Atom Name

The atom name contains 4 characters. Names with X or Y in them have special significance and are used, especially, to close rings. These special atoms act as ghosts of the atom which is named without the X or Y, and they will have the same position as the real atom during regularisation.

The Backward Chain

The chain values act as pointers to atoms defined in the dictionary. For example, the value 1 signifies the first atom in the residue being described, and 5 would be the fifth. The backward chain represents a connection from the present atom (call it the i'th) to an earlier atom in the list (call it the h'th). It signifies a connection between the present atom and a later atom in the list (call it the j'th). Then i is less than j and there must be no backward chain connections to atom i between the i'th and j'th atoms in the residue. It signifies a connection between the present atom and a later atom in the list (call it the k'th). Then there can be no backward chains to i from atoms in the list beyond k. There can be other connections to the i'th atom from atoms in the list between positions j and k, but these will be described by backward chains.

The Bond Length

It is the value for the bond defined by the backward chain from this atom.

The Bond Angle

It is the value of the bond angle defined by 2 backward chains from this atom. It is the value of the torsion angle defined by 3 backward chains from this atom.

The Torsion Angle Flag

It takes the value 0 for fixed dihedrals and greater then 0 for flexible ones. The angle concerned is best described with an example: The angle PHI for an Amino Acid is defined by the atoms C, N, CA, C. It is flexible and its flag is carried around with atom CA. Likewise, PSI is defined as flexible at atom C and OMEGA at atom N.

The Complication

This comes for atoms with more than one forward chain. The highest forward chain atom is straight forward. The torsion angle value held at the lowest forward chain atom now takes on a special meaning and defines how much this atom is out of the plane defined by h, i and k as defined above. In particular, if we hold h towards us and look down the i to k bond, it is the angle made by line hi and ij in projection. It is quite easy to get this value wrong by 180 degrees (or wrong sign) when making a new type of residue.

Warning

This is meant as a help to someone who has to make a new entry in the dictionary. It is not a full description. You are advised to look at the existing entries and draw out how they have been built up. With a little practise it is not difficult, honest. The distributed version skips over all atoms begining with `H'.