Molscript is a program made by Avatar Software AB for producing representations of 3D molecular structures, and is usually (but not exclusively) used for making schematics of proteins. It uses shapes such as helices, cylinders, spheres, coils, etc. to represent various elements of the protein's structure, to which properties such as colour and transparency can be applied. These are specified by a (rather unfriendly, in my opinion) scripting language which tells MolScript how to process a file of atomic coordinates as well as specifying the position of the camera and lights. Objects produced by other programs, such as molecular surfaces, can also be included in images.

A small program called MolAuto is used to automatically produce MolScript input files from the structural information in PDB files. MolScript then converts these into images in PostScript, VRML, Raster3D, interactive OpenGL, and various bitmap formats.

The current version is v2.2.1 and was released in 1999. It is distributed as source and IRIX binaries, and requires a license. Its academic use is currently free. More information can be found at