Molecular Graphics Systems

The first pure molecular graphics system followed after a few years. It was built in 1970 by Langridgc at Princeton University 195], The system was based on the Picture System 2 of Evans and Sutherland and could also display bonds and colored atoms. 

The disadvantage of molecular mechanics is that there are many chemical properties that are not even defined within the method, such as electronic excited states. Since chemical bonding tenns are explicitly included in the force field, it is not possible without some sort of mathematical manipulation to examine reactions in which bonds are formed or broken. In order to work with extremely large and complicated systems, molecular mechanics software packages often have powerful and easy-to-use graphic interfaces. Because of this, mechanics is sometimes used because it is an easy, but not necessarily a good, way to describe a system. 

DeLano WL (2002) The PyMOL molecular graphics system, DeLano Scientific, Palo Alto, CA, USA... 

This decade also saw the first major developments in molecular graphics. The first multiple-access computer was built at MIT (the so-called project MAC), which was a prototype for the development of modern computing. This device included a high-performance oscilloscope on which programs could draw vectors very rapidly and a closely coupled trackball with which the user could interact with the representation on the screen. Using this equipment, Levinthal and his team developed the first molecular graphics system, and his article in Scientific American [25] remains a classic in the field and laid the foundations for many of the features that characterize modern day molecular graphics systems. 

DeLano, W. L. (2002). The PyMol Molecular Graphics System. DeLano Scientific, San Carlos, CA. 

Crestfield, A. M., Stein, W. H., and Moore, S. (1963). Properties and conformation of the histidine residues at the active site of ribonuclease./. Biol. Chem. 238, 2421-2428. DeLano, W. L. (2002). The PyMol Molecular Graphics System. DeLano Scientific, San Carlos, CA. 

W. L. DeLano, The PyMOL Molecular Graphic System-, DeLano Scientific LLC Palo Alto, CA, 2006. 

Figure 2.21 Zinc coordination sphere in a zinc-finger protein from the synthetic construct corresponding to Xenopus Xfin-31 domain from PDB IZNF. Visualized using The PyMOL Molecular Graphics System and ChemDraw Ultra, version 10.0. (Printed with permission of Delano Scientific, LLC and CambridgeSoft Corporation)...

Computer and molecular graphic system (See Chapter 5 in the nitrogen stream. 

Figure 9. The structure of GCAP3 (Stephen et at., 2006). Residues that correspond to pathogenic mutations in GCAP1, the structure of which is unknown, are shown in yellow with the side chains. Ca2+ is shown as yellow spheres. Molecular graphics representations were created with PYMOL (Warren L. DeLano The PyMOL Molecular Graphics System. DeLano Scientific LLC, San Carlos, CA, USA. http //www.pymol.org) (See Colour Plate 9)...

Fio. 1. (a) A view of the influenza virus hemagglutinin trimer showing jV-acetylneuraminic acid (3, in CPK form) bound, (b) The tetrameric unit of influenza A virus sialidase. The figures were generated using the PyMOL Molecular Graphics System (Delano, W.L. (2002) at http // www.pymol.org). 

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