Molscript

From MarcsHomepage

Introduction

Molscript, written by Per Kraulis, is a PDB-to-Postscript converter, which can generate Jane Richardson-style ribbon-models from PDB data. This is very useful for smaller black and white drawings or resizeable vector-images. Version 2.1-which is a completely rewritten version of Molscript (in C instead of Fortran) has the ability to display and render raster-graphics with help of a interactive OpenGL-graphics-interface.

User Interface

Molscript1.jpg

Molscript reads in a PDB file together with a script which selects the appropriate parts of a molecule for ribbons, strands or detailed atomic display. You can also specify the radius of an atom-representation, highlight parts by coloring them according to various schemes (CPK for example) or add labels. In version 2 there is an additional program called Molauto, which produces a useful initial view of the molecule, which can be refined interactively afterwards. Molscript features a somewhat strange selection-language (at least, I prefer what Roger A. Sayle has created for Rasmol over all the other solutions in this whole review), version 2 has up-to-date coloring and rendering options (shading and display of smoothly colored ribbons, import of external objects, selective ball/stick-rendering of single atoms, residues and so on).
Molscript was originally intended for use on a SGI-computer. It can (with some adaption) be successfully compiled for almost every other UNIX-flavour and even the command-line under Windows.
The new 2.1-version is a complete rewrite in ANSI C, which should be compilable on almost every system which features a ANSI C compatible compiler and an OpenGL-compatible graphics library (only necessary for the raster-output-options and for interactive viewing of the molecule).
Registration of Molscript is free for academic use.
There exist a somewhat incomplete interfaces from Rasmol with it's more sophisticated real-time-manipulation capabilities, which means you don't have to learn Molscripts command-language if you aren't a frequent user of the program.
There is a commercially available modelling-program called Spock which can export Molscript-2.0 commands, and which may be usable as Molscript-front end.

Features

  • generation of colored/shaded Jane Richardson style ribbon plots
  • various volume representations for single atoms/molecules (CPK, ball-and-stick)
  • coloring of individual residues
  • free placement of labels (alphanumeric)
  • script-like input-language
  • reads various 3D-molecule-formats
  • output to PS or EPS as well as various raster-formats
  • output of data for the free rendering program Raster3D (of minor interest to me as there are excellent Povray-dependent programs elsewhere (see review of Molmol and SwissPDBViewer, although the rendered images look very good).