Structure display program

Molscript A program for displaying molecular 3D structures in both schematic and detailed representations, http //www.avatar.se/molscript/. 

SemiChem products are available at http //www.semichem.com. AMPAC , available as a stand-alone product with Windows-based and workstation level interfaces, is a semiempirical quantum mechanical program featuring SAMI, AMI, MNDO, MNDO/d, PM3, MNDO/C, MINDO/3 semiempirical methods. AMPAC also includes a graphical user interface (GUI) that builds molecules and offers full visualization of results. The SYBYL/Base program offered by Tripos, Inc. (products described below) provides an interface with interactive graphing and structural display tools that can be used to access AMPAC s calculation tools. 

Dowty, E. (1991) ATOMS. A computer program for displaying atomic structures. Copyright E. Dowty, 122 pp. 

Koradi R., Billeter M. and Wuthrich K. (1996) MOLMOL a program for display and analysis of macromolecular structures. J. Mol. Graphics 14, 51-55. 

The software used to produce many of the crystal structures displayed in this book was CaRIne v. 3.1. This is an easy to use program, most suited to inorganic crystal structures. A later version, CaRIne v 4.0, is under development. 

By this time the basic standards for such a program, in terms of structure input, query input, substructure search and structure display capabilities were quite well established and, by and large, we were satisfied that all programs could meet these requirements. We therefore focused on the aspect that would have the heaviest bearing on our small development effort the ease with which a program might be integrated into ABACUS. 

The merit of this approach is that it gives us access to structure display on virtually any document, regardless of what program produces it. We have yet to explore this avenue fully but there could well be many applications outside the ABACUS system. 

With the graphical output program in place, it was possible to provide our scientists with the first fruits of the early SOCRATES system graphical structure display at a terminal of compounds from the company files (generated fi om the stored WLN s via connection tables). The next step was to provide a structure match capability. As mentioned earlier, within INDABS there already existed a fast chemical novelty search which employed an index of topological codes. This was easily integrated into SOCRATES to accept graphically drawn structures fi om SENTRY instead of WLN s. 

The necessary modifications to the atom-by-atom search program and to the structure display program have been carried out. In the case of atom-by-atom search we have included the facility to indicate the bonds in the substructure which have been formed/brcken. This means that all types of substructure can be searched for and any part of that substructure may be the reaction site. Both reactant and product molecules can be searched so that the following questions can be answered ... 

Modifications have been made to the structure display program. Here the bonds broken or formed are marked on the structure of the total molecule. Bonds formed are marked with a circle and bonds broken with a slash mark, so imitating a chemists normal presentation. 

In the past, it would take months or years to determine the structure of a protein molecule now it takes a day or even a few hours. Since the wavelength can be changed easily and the intensity of an x-ray is much brighter, more data can be collected. By analyzing the diffraction pattern using software, it becomes much simpler to make a map of the electron density in the crystal. Programs are available or may be devised to have the shape and the structure displayed on a computer screen as a mass of squiggly lines, ribbons, and little balls. 

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