Table of Contents{1} Different Concepts of Molecular Structure {3} There are some obvious differences... {4} Compared to the Quantum Mechanical Model... {5} In spite of these things... {6} Simplest structure representation describes... {7} Note: Just knowing where the atoms are may not be enough {8} Explicit connectivity, can clearify which atoms go together {9} The absolute positions of the atoms depend on the orientation and position of x,y,z =0,0,0 {10} Indeed, we only need the relative position of each atom to the others. {11} Bond length, r, and the bond vector, R. {12} The angle between three atoms (1,2 & 3): {15} Such measurements give internal coordinates {16} The concept of Atom Types {17} The concept of atom types... {18} Atom typing is used to ... {19} Some examples of atom typing... {20} Some examples of atom typing... {21} Thus, for a computational program to use PDB structures... |
Author: John E. Wampler
Email: wampler@bchiris.bmb.uga.edu Home Page: http://bmbiris.bmb.uga.edu/BMB8200 References: Abola, E. E., Bernstein, F. C., Bryant, S. H., Koetzle, T. F., and Weng, J. (1987) Protein Data Bank, in Crystallographic Databases - Information Content, Software Systems, Scientific Applications (F. H. Allen, G. Bergerhoff & R. Sievers, eds.) Data Commission of the International Union of Crystallography, Bonn, pp. 107-132. |