Computer graphics interface

Molecular mechanics has become a standard method in computational chemistry and is extensively used to solve problems in organic chemistry, in medicinal chemistry, and in many other areas of chemistry. Today, sophisticated computer graphics interfaces are generally used in connection with molecular mechanics calculations. The molecule to be studied may conveniently be constructed on the computer screen and the setup for the calculation may be done simply by choosing one or several computational options displayed by the graphics interface. In addition, various molecular mechanics methods are implemented on personal desktop computers or small workstations. This technological advance has drastically increased access to molecular mechanics calcu-... 

With the widespread use of computer graphics interfaces in connection with molecular mechanics calculations and the large number of different molecular mechanics methods available, the major problem today is not how to set up and perform the calculations but which method (or force field) to use for the problem at hand. A related question for the newcomer to molecular modeling is which software to buy. Each software package has at most only a few of the many different force fields, and no one force field is common to all programs. 

Examples of graphics applications interface standards are the Graphics Kernel System (GKS) (i6) and the Programmer s Hierarchical Interactive Graphics System (PHIGS) (7) Specific interface definitions are part of both GKS and PHIGS. For the device driver interface, examples are the North American Presentation Level Protocol Syntax (NAPLPS) ( ) and the Computer Graphics Interface (CGI) (9). 

The most general device driver interface is the Computer Graphics Interface (CGI, called "VDI" in Europe) CGI will standardize device drivers, making all graphics devices appear to be identical by defining an interface to a virtual (ideal) device This standard interface protocol is converted to the actual form for a real device in the host (with a device driver) or in the graphics device itself. 

UniChem (we tested Version 4.1) is a graphic interface made for running calculations on remote machines. The UniChem GUI runs on the local workstation and submits the computations to be run on a remote machine. The server software comes with MNDO, DGauss, and CADPAC. It can also be used as a graphic interface for Gaussian and Q-Chem. A toolkit can be purchased separately, which allows users to create an interface to their own programs. 

Babel (we tested Version 1.6) is a utility for converting computational chemistry input hies from one format to another. It is able to interconvert about 50 different hie formats, including conversions between SMILES, Cartesian coordinate, and Z-matrix input. The algorithm that generates a Z-matrix from Cartesian coordinates is fairly simplistic, so the Z-matrix will correctly represent the geometry, but will not include symmetry, dummy atoms, and the like. Babel can be run with command line options or in a menu-driven mode. There have been some third-party graphic interfaces created for Babel. 

As computer programs evolve they become easier to use. Modem programs often communicate with the user in terms of a graphical interface, and many methods have become essential black box procedures if you can draw the molecule, you can also do the calculation. This effectively means that you no longer have to be a highly trained theoretician to run even quite sophisticated calculations. 

Pazos, F., Olmea, O., and Valencia, A. (1997) A graphical interface for correlated mutations and other protein structure prediction methods. Comput. Appl. Biosci. 13, 319-321. 

The adsorption of protein from single component solutions is qualitatively understood, although a quantitative understanding and models or theories with predictive character are not yet available. If the structure and solution properties of the protein are known and if the solid-buffer interface properties are known, then by careful examination of the surface of the protein (ideally via molecular computer graphics), we can indeed predict what orientation of the protein is preferred on that particular surface. 

Probably, the most important tool of computational chemistry is computer graphics because this provides the interface between the user and the computer. Molecular structure is the universal language of chemists. Therefore, it was an important advance when a user could enter a molecular structure into the computer by simply drawing lines and pointing and clicking on a building menu. 

Fig. 4. Computer graphics of the domain interface building the channel to the active center in PDC. The thiazolium ring of ThDP is visible at the bottom of the channel. A tryptophane residue (blue) has been engineered into the crystal structure of PDCS.u. by means of computer graphics. The picture was generated by J. Grotzinger using the program GRASP [181]...

---