Introduction

An Efficient General-Purpose Least-Squares Refinement Program for Macromolecular Structures

Dale E. Tronrud, Lynn F. Ten Eyck, and Brian W. Matthews Institute of Molecular Biology and Departments of Chemistry and Physics University of Oregon Eugene, OR 97403, USA Received: 16 July 1986 Accepted: 12 November 1986

Abstract:

A package of programs has been developed for efficient restrained least-squares refinement of macromolecular crystal structures. The package has been designed to be as flexible and general purpose as possible. The process of refinement is divided into basic units and an independent computer program handles each task. Each functional unit communicates with other programs in the package by way of files of well defined format. To modify or replace any program, the user need only understand the function of that particular element. Stereochemical restraints are defined in a general way that can be applied to proteins, nucleic acids, prosthetic groups, solvent atoms and so on. Guide values for bond lengths and bond angles are specified in a straightforward direct manner. Designated groups of atoms can be held constant or constrained to behave as a rigid body during refinement. In order to make the package as efficient as possible, the fast Fourier transform algorithm is used for all the crystallographic transformations. To highlight potential errors in the refined structure the user can list those atoms that have the worst bond lengths and angles, or have the largest positional, temperature-factor or occupancy gradients. It is also possible to check that protein and solvent atoms do not sterically clash with symmetry-related neighbors. Applications of the program package to a bacteriochlorophyll-containing protein, thermolysin-inhibitor complexes and mutants of bacteriophage T4 lysozyme are described.

 

• Introduction
• Feature and organization
• Overall organization
• Data input and data transfer
• Geometry definition
• Rigid-body refinement
• Detection of errors in the model
• Theoretical background
• Crystallographic term
• Stereochemical term
• The control program
• Applications
• Bacteriochlorophyll a protein
• Thermolysin-inhibitor complexes
• Bacteriophage T4 mutant structures
• Efficient calculation of gradients by means of the fast Fourier transform algorithm
• Definitions
• Lifchitz variation of the FFT algorithm
• The reduction of series termination errors
• Generalized uses of the algorithm
• Evaluation of the gradients of the terms necessary for the implementation of stereochemical restraints
• Introduction
• Bond lengths
• Bond angles
• Torsion angles
• Planarity
• References
• About this document ...

Thu Jan 22 14:07:35 PST 1998