AVS software for visualization in molecular microscopy

AVS (Application Visualization System) is commercially available software for analyzing and viewing data. AVS is primarily used in the physical sciences and engineering, and here we describe the application of AVS for examining three-dimensional density maps generated by electron microscopy and image processing. For this purpose, AVS can be applied with relative ease, even though the software is indeed quite sophisticated. The primary advantage is that visualization applications can be generated by combining software components, called modules, into executable flow networks. Simple networks are described for generating ribbon diagrams of macromolecules, surface-shaded views, and contour maps. Easy to use dials, bar sliders, and buttons provide tremendous versatility for real-time manipulation of isosurface values, depth cueing, view orientation, size, and animation. In addition, AVS supplies a framework for building new modules in C or FORTRAN. Modules for excavation and cropping provide tools that are particularly useful for extracting segments of a map and for examining maps of supramolecular complexes such as viruses. We describe a number of modules we have designed for analysis of three-dimensional data sets, as well as modules for importing image data from other software packages into AVS. We also describe xformat, a stand-alone file conversion utility designed to allow import of a variety of image and map file formats into AVS.