Edit

Delete restraints

This command removes energetic restraints imposed on the model.

Overlay

Calculates a standard deviation and/or makes the superposition of two parts - selected and not selected. The corresponding atoms are determined in order of their succession in the selected and unseparated parts.

Detect mode serves for iterative overlay. Only those atoms that are already close are superimposed. The procedure can be repeated several times.

Geometry

This module measures the distances, angles, dihedral angles, and coordinates. It operates points in the three-dimensional space specified by Cartesian coordinates, positions of atoms, or positions of molecular centers-of-mass. The parameters can be both measured and altered by the user. Using the module is described in the Geometry editingsection.

Move model

This command moves the whole model in space.

The same panel also appears when the File > Add command is activated. This can be useful to separate the current and added models in space.

Disorient selected molecules

Rotates the selected molecules around their centers of mass at a random angle. The command is useful for the rapid preparation of fluid models from an ordered structure, for example from molecules on a lattice.

Delete atoms

Deletes the selected atoms.

Delete selected bonds

Deletes the selected bonds.

Bind two molecules using selected hydrogens

Remove two hydrogen atoms and form a chemical bond. Partial charges are transferred from the hydrogen being removed to the atoms of the opposite molecule. Thus, the total charge does not change.