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Moloc: Molecular Modelling on UNIX Workstations: 11 Topology Changes, Building [dTp]

Topology Changes, Building [dTp]

This is the basic modelling facility to build and modify united- (or all-) atom structures. Most activities are changing the topology of the structures, although the forge menu can also be addressed from here.

Add and Delete Atoms, Change Core Numbers

Atoms may be attached to existing ones, by picking those (left button). If attachment can be done in more than a single conformation, the user can toggle through the various possibilities by keeping the left-hand button pressed and repeatedly pressing the middle button. After releasing the left button this feature is lost. An atom picked with the middle button will be removed. The type of the added atom is indicated as the menu header. The type of bonding (single, double, triple) applied is also indicated (1, 2, 3). Regarding atom types, there is no distinction into various subtypes for the same chemical symbol! This must not be considered a drawback, because the force field makes proper recognition and treatment.
If the bond type indicator is set to (c) atoms types are changed by picking. The type they are changed to is given in the menu header. Some changes may be awkward with respect to Hydrogen counts. Consequently, these counts should be checked afterwards!

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