A modeling project is completly described by an assembly of Fragment Generators. Those Fragment generators are organized in what we call a FG hierarchy. A FG A is said to be subordinate to a FG B if A is placed under B's control, i.e. if B uses A to construct sub-parts of its fragment. In this case, B is called the supervisor of A. Such a subordinate FG is also said to be a lower level FG than its supervisor.
In fact, the FG hierarchy precisely specifies the building order (in what order the fragments are placed according to each other) of the structure. It also specifies the method chosen by the user to generate the different fragments. A FG is said to be closed if it does not depend on any other FG. FG A depends on FG B if all residues represented by B must be placed before A can place its own residues. Consider the folowing simple example: One wants to place res1 relatively to res2 according to a given spatial relation. It is essential to first assign a conformation and a location in space to res1. Then a conformation can be assigned to res2 and it can be placed in space according to the relation.
The above example illustrates what we call the Consistency of the FG hierarchy. Generally speaking, a FG is said to be consistent if all it needs is available before one calls Advance on it. We already said that the building order is completly defined by the FG hierarchy. Then so is the consistency of the hierarchy. This property allows MC-SYM to scan the FG hierarchy for irregularities and to prompt the user if any are detected.
The available FGs and the way to use them are depicted in Section 4 below.