MOSBY

(MOlecular Structure Browser with analYsis)

MOSBY is a program to view atomic structures of protein molecules. Beyond its basic molecular graphics functions, extension modules provides custom functions for research works in structural biology and computational molecular biology. It was developed on UNIX workstations and now ported to Windows and Macintosh computers.

CURRENT DEVELOPMENTS

It was under a major model change using the Lua langauge as a main infrastructure of the graphical application program. This change allow following new functionalities.

• Scripting support --- a set of command is provided for molecular rendering.
• Simple drawings --- simple graphics primitives are available to annotate molecular figures.
• Anaylsis scripts ---- a script program for a calcuration using atomic coordinates of the molecule.

A new software distribution is under preparation.

EZLUA is an experimental wrapper functions for Lua API. It was used for this software development. Please follow the link for details.

BASICS OF MOSBY

In using MOSBY, most operations are in the main menu bar on top of the window. Items in the tool bar at the left side select the mode of mouse operation. Basic functions of atomic coordinates of proteins includes:

• Molecular models of wire frame, ball & stick, tube and space filling.
• Real-time viewing manipulation of molecules by mouse operations with depth-cueing, clipping, scroll, and perspective.
• A sequence window provides the amino acid sequence view of the protein. The selection of residue also cooperates with the molecular model window and vice versa.

The graphics rendering is reasonalbe both quality and speed on most conventional workstations or personal computers. The rock animation with four cyclic frames provides smooth horizontal rotation that is independent of the number of atoms. Additionally, the qualities of cylinder and sphere were improved by introducing edge lines between primitives far in depth.

EXTENDING MOSBY

There are several plug-ins to enhance functions of MOSBY.

• An Electron Density Plug-in. This module reads an electron density map file and visualizes the isosurfaces of density function into the molecular model by an algorithm similar to the marching cube. The plug-in has a dialog box for the parameter set of isosurface values that is prepared in a file. By trapping an order function o the rendering atomic model, the plug-ins depict various kinds of pictures into the molecular model window.
• A Superposition Plug-in. With specified two sets of atoms defined as molecular groups in our browser program, the coordinates of the first group are translated to fit those of the second. Since the plug-in only describes its algorithm, it is easy for users to customize or replace it. Furthermore, functions for editing atomic data in our browser enables another plug-in of molecular modeling with a customi ed graphical user interface.
• Filter Plug-ins. The browser program loads the filter plug-ins which access atomic data in different kinds of formats. A filter plug-in defines a new order that is a function of the filter and registers it into the list of filters. A new format is supported simply by modifying an existing sample filter.

MOSBY uses the dynamic linking method, so that extension modules act as if it is a part of the host program. Actually, detailed method and interface to MOSBY are rather complicated, we can take a source code of those plug-in modules as a template to make another extension module.

DISTRIBUTION

MOSBY is a software copyrighted by AIST. An academic license to use this software is provided without fee. Please contact to us about another license for the commercial use.

README

a gzipped tar archive --- beta (ver 0.955)

--- Our software distribution server is now under rework. This is a tarball of our beta release dated 2007 Jan. Porting information about Windows and MacOS are also provided. Please excse us for stopping a service from the previous website at http://www.etl.go.jp/~ueno/bioinfo/mosby/

A SNAPSHOT OF MOSBY

OVERVIEW OF THE SOFTWARE ARCHITECTURE

Last updated : Jun 2 2008