Translation, computer graphics

Picture transformations (e.g. rotation, translation, scaling, perspective etc) in interactive computer graphics lend themselves naturally to representation in matrix notation, and implementation of the various algorithms on a vector processor is obviously straightforward and very worthwhile (particularly if moving pictures are required.). For this reason graphical applications of the MVP-9500 will not be discussed here and the interested reader is referred to one of the standard texts in this area (7). 

To define the structure of a molecule in a precise manner then, we must create a list (the order is not important) of atomic coordinates Xj, yj, Zj (and here the order is important). A molecular structure becomes a set of ordered triples Xj, yj, Zj, one for every atom. This is imminently suitable not only for translation into a visual representation, but for manipulation and analysis in a computer, and presentation on the screen of a computer graphics workstation in any number of manifestations. 

Even the most basic computer graphics program provides some standard facilities for the manipulation of models, including the abihty to translate, rotate and zoom the model towards and away from the viewer. More sophisticated packages can provide the scientist with quantitative feedback on the effect of altering the structure. For example, as a bond is rotated then the energy of each structure could be calculated and displayed interactively. 

For several years, operating systems were character based. They displayed information on the screen in text format and people interacted with them using command words. Then, a couple of people at the Xerox Palo Alto Research Center (PARC), intrigued with the idea that computers should be friendly and easy to use, started working with a graphical user interface (GUI), which used pictures to represent computer entities (like files, disks, and so on). To interact with the pictures, a special device was introduced into the computer world. This device was the mouse. The mouse translates movements on a horizontal surface into movements of a pointer on the screen. There are two methods of making these translations opto-mechanical and optical. 

It is possible, as shown by Rossmann and Blow (1962), to search for redundancies in Patterson space that correspond to the multiple copies of molecular transforms. Rossmann and Blow show, however, that the Patterson map does not need to be computed and used in any graphical sense, but that an equivalent search process can be carried out directly in diffraction or reciprocal space. Using such a search procedure, called a rotation function, they showed that noncrystallographic relationships, both proper and improper rotations, could be deduced in many cases directly from the X-ray intensity data alone, and in the complete absence of phase information. Translational relationships (only after rotations have been established) can also be deduced by a similar approach. Rotation functions and translation functions constitute what we call molecular replacement procedures. Ultimately the spatial relationships among multiple molecules in an asymmetric unit can be defined by their application. 

The structure, input graphically by the chemist, was translated into a conneaion table, which was the form used internally by the computer. Each atom and bond drawn in by the chemist was thus understood by the computer as a table of information about the atom or bond. For example, an atom table consisted of the atom s charge, the number of valences used, the number of atoms attached, the atom type, and the names of bonds to the atom. A bond table told whether the bond went up or down, the bond type (i.e., single, double, triple), and the names of the atoms the bond was between. In addition, the atoms position coordinates were stored separately. ... 

Concepts of visual reality and virtual reality are sometimes confused. Virtual reality is a sophisticated computer description of real-world conditions in the virtual world. It cannot communicate directly with humans because it has been developed for the purpose of communication between computer procedures in the form of data structures. Visual reality is the tool that converts these data structures into graphic or other understandable forms in order to visualize computer descriptions for humans. Concepts and intents originate in humans in visual form visual reality is the tool to translate them into a form understandable by computer procedures. Two-way interactive graphics-based communication is applied. Virtual and visual realities are key techniques for the representation of engineering objects and communication of represented information between humans and procedures in virtual worlds. 

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