GEOMETRY
Stereochemical Program
This program takes a coordinate file and a definition of the ideal geometry for that structure and calculates the function value and the first and second derivatives with respect to the positional parameters of the atoms. It can also provide various statistical measures of how closely the molecular model obeys the ideal geometry restraints. The stereochemical restraints this program understands are bond lengths, bond angles, torsion angles, pseudorotation angle of five membered rings, planarity about a trigonal atom, general planarity, non-bonded contacts, B correlation, and chiral centers. Chirality is a two state, discontinuous function and therefore cannot be refined. The program informs the user when an atom with incorrect chirality is encountered.
The program has functions beyond that of refinement. With the SCREEN command one can determine the places in the model with the greatest disagreement with standard geometry. The REPORT GEOMETRY command can be used to compare the average and standard deviation for each geometry restraint, as determined by actually looking at coordinates, with any particular library. This allows one to generate new libraries, or look for errors in the existing ones.