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The commands in this section can be used to construct cartesian coordinates from internal coordinate values. The internal coordinate data structure can also be used for analysis purposes. There are flexible editing commands for manipulating the data structure.
{IC } { SETUp }
{BUILd} { FILL [COMP] }
{ EDIT }
{ BILD [COMP] }
{ SEED atom atom atom [COMP] }
{ }
{ { DELete } { BYNUM int [int] } }
{ { KEEP } { atom-list-spec } }
{ }
{ DIFF [COMP] }
{ PURGe }
atom ::= residue-number atom-name
See section Atom Selection, for a description of the `atom-list-spec'.
The syntax for the EDIT subcommands are:
{ [DISTance] atom atom real }
{ [BOND ] }
{ ANGLe atom atom atom real }
{ DIHEdral atom atom [*]atom atom [DELTA] real }
{ END }
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:
DISTance atom atom real ANGLE atom atom atom real DIHEdral atom atom [*]atom atom real END atom::=residue_number atom_typeThe 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.
Given the positions of any three atoms, the position of a fourth atom can be defined in relative terms (internal coordinates) with three values: a distance, an angle, and a dihedral specification. Where many atoms are connected in a long sequence (as in proteins) it is easiest to consider four atoms in a chain. If the positions of one end of the chain is known, it is possible to find the positions of all of the remaining atoms with a series of internal coordinate values. But in the more general case, where some central portion of a molecule is known it is necessary to be able work in both directions. This lead to the present form of the internal coordinate data structure (five values for four atoms) where if either endpoint is unknown and the other three atoms are determined, the position of the end atom can be found. The improper type of internal coordinate data structure was created for branching structures (as opposed to simple chains). Since there are roughly five values in the data structure for every atom it is clear that the positions are overspecified Keep this in mind when externally editing IC files. The program will use the first acceptable value when building a structure and ignore any redundancies. The EDIT commands will always modify all occurrences of each edited parameter.
The internal coordinate file can be stored in either card or binary
form. for most purposes the card form will be used (since it can be
edited). There are two types of elements in the internal coordinate
file, those that correspond to normal dihedral angles and those that
correspond to improper dihedrals. They can be distinguished by the
presence of a '*' just before the iupac name of the third (k) atom (its
presence denotes an improper dihedral type). For each element there are
four atoms (referred to as I,J,K,L) and five
values. The values for ordinary elements correspond to: R(IJ),
THETA(IJK), PHI(IJKL), THETA(JKL), and R(KL)
respectively. For improper dihedral types, the values are: R(IK),
THETA(IKJ), PHI(IJKL), THETA(JKL), and
R(KL). Notice that for the second type that the K atom is at the
center of both angles. Elements of the IC file are symmetric with
respect to inverting the order of the atoms except that for improper
types only atoms I and L can be interchanged (also the sign of
PHI must be changed since PHI(IJKL) = -PHI(LJKI).)
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