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Moloc: Molecular Modelling on UNIX Workstations: 16 Surfaces and Loci [srf]

Surfaces and Loci [srf]

Surfaces can be calculated or generated, either as dotted surfaces or as polyhedra, according to the users choice. By default, van der Waals surfaces are taken, but an additional solvent radius can be added (option r). Included are all visible entries, but a surface is only generated or calculated for the atoms chosen in the set menu. If only a fraction of the visible atoms is chosen, one has the choice of counting overlaps between all atoms of an entry, or only between atoms belonging to the set. The generated surfaces are associated entries to the one containing the central atoms. They can be deleted in exactly the same way as normal entries. Upon moving the central atoms, the coordinates of the surface are not updated. The surface calculation is approximative and improves with increasing number of points per atom.
Further options related to surfaces are: generation of loci, calculation of free energy of solvation, estimation of free energy of binding, and location of voids.

16.1 Loci [loc]

Loci of points can be generated. The points correspond to positions which specified atoms assume under rotation about specified bonds. The labels of the points indicate the state of the rotation, that generated the point. Each character indicates the number of rotation steps performed about a bond, where the first character corresponds to the bond nearest to the atom. For step numbers above 10 the letters of the alphabet are used. The loci are either displayed as dots or as a net of bonds connecting each pair of points separated by a single rotation step (default).

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