This module analyzes the agreement between the present model's stereochemistry and ideal geometry. The precise functional form of this term is the sum of the square of the deviation from ideality for every bond length, bond angle, torsion angle, pseudorotation angle, trigonal carbon, general plane, and temperature factor correlation. It also adds in the sum of the square of the difference between the minimum distance allowed between two non-bonded atoms and the distance actually found whenever the two atoms are too close together.
A feature of this module is that any geometry restraint can span between a molecule in the asymmetric unit and one in a neighboring asymmetric unit. This ability is useful for keeping solvent molecules on the surface in line, and restraining the geometry of cross-links, or larger solvent molecules which sit on special positions.
All of the functions of this module are completed with the program Geometry. To perform the calculations required for a long loop one would use either the CURVATURE or GRADIENT command. In a short loop the FUNCTION command should be used because it causes only the function value to be calculated.