Open AccessSaxsMDView : a three‐dimensional graphics program for displaying force vectors
Author(s) -
Kojima Masaki,
Kezuka Yuichiro,
aka Takamasa,
Hiragi Yuzuru,
Watanabe Takeshi,
Kimura Kazumoto,
Takahashi Kenji,
Yanagi Shigeru,
Kihara Hiroshi
Publication year - 2008
Publication title -
journal of synchrotron radiation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.172
H-Index - 99
ISSN - 1600-5775
DOI - 10.1107/s0909049508015951
Subject(s) - molecular graphics , representation (politics) , small angle x ray scattering , computer graphics , force field (fiction) , graphics , computer science , object (grammar) , molecular dynamics , computational science , dipole , computer graphics (images) , field (mathematics) , scattering , crystallography , physics , chemistry , artificial intelligence , computational chemistry , optics , mathematics , pure mathematics , quantum mechanics , politics , political science , law
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.