SaxsMDView: A three-dimensional graphics program for displaying force vectors

Abstract

A new three-dimensional graphics program, SaxsMDView, is described. The program performs a three-dimensional graphical representation for protein molecules along with the force vector (or vector potential) applying to each atom. The displayed object can be rotated and translated in arbitrary directions by interactive mouse manipulation. While SaxsMDView was originally intended to visualize the result of SAXS_MD, a previously developed program based on the restrained molecular dynamics with small-angle X-ray scattering constraints, it can also be useful for graphical representation of other objects such as coarse-grained molecular models reconstructed by ab initio modelling or solvent site-dipole field vectors induced around the protein molecule. Some examples of the application of the program including the graphical analyses of the results with SAXS_MD are also presented. © 2008 International Union of Crystallography.