Section 25.2.7.1. Introduction

Visualization of the atomic coordinate data obtained from a crystallographic study is a necessary step in the analysis and interpretation of the structure. The scientist may use visualization for different purposes, such as obtaining an overview of the structure as a whole, or studying particular spatial relationships in detail. Different levels of graphical abstraction are therefore required. In some cases, the atomic details need to be visualized, while in other cases, high-level structural features must be displayed.

In the study of protein 3D structures in particular, there is an obvious need to visualize structural features at a level higher than atomic. A common graphical `symbolic language' has evolved to represent schematically hydrogen-bonded repetitive structures (secondary structure) in proteins. Cylinders or helical ribbons are used for α-helices, while arrows or ribbons show strands in β-sheets.

The domain of the MolScript program is the production of publication-quality images of molecular structures, in particular protein structures. The implementation of MolScript is based on two design principles: First, the program must allow both schematic and detailed graphical representations to be used in the same image. Second, the user must be able to control the precise visual appearance of the various graphics objects in as much detail as possible.

The original version of MolScript was written in Fortran77 and produced only PostScript output (Kraulis, 1991). The current version (v2.1.2, as of January 1999) has been completely rewritten in the C programming language. The new version is almost completely compatible with previous versions. The main new features in version 2 are several new output formats, the interactive OpenGL mode (see below) and dynamic memory allocation for all operations.

This section reviews the basic features of MolScript. Detailed information about the program, including instructions on how to obtain the software, can be found at the official MolScript web site http://www.avatar.se/molscript/ , where the online manual is also available.