Multi-platform software package for biomolecular visualization and modeling. Bodil is a modular, multi-platform software package for biomolecular visualization and modeling. Bodil aims to provide easy three-dimensional molecular graphics closely integrated with sequence viewing and sequence alignment editing. Functionality of Bodil is implemented in dynamically loaded modules.

Most of the modules available in the present release provide visualization tools, with protein modeling, small-molecule ligand docking and other modules being currently under development. New modules can easily be added via a documented C++ application programming interface.

Bodil is written in standard C++ using the Qt application development framework and OpenGL 3D graphics. The software has been ported to Linux, SGI Irix and Microsoft Windows NT/2000/XP platforms.

Bodil Features:
1. Multi-view 3D graphics
2. Stereoscopic viewing using CrystalEyes goggles (or equivalent) is supported on both SGI Irix and Intel Linux.
3. Integration of sequence viewing and alignment editing with 3D molecular graphics
4. A hierachichal tree view to chemical data
5. Molecular surface calculation and visualization
6. Visualization of electron density and Grid / AutoDock / DelPhi maps
7. Fully automatic protein structure superposition using a C-alpha packing profile correlation
8. Modular architecture: dynamically loaded plugin modules, application programming interface based on standard C++

Bodil has three kinds of views to molecular data: a hierarchical tree view (left), three-dimensional molecular graphics (right) and a sequence alignment view (bottom). All views show the same objects. When e.g. a column of the sequence alignment is selected, the corresponding residues of each structure in the alignment become selected (green) in the molecular graphics view, too.

Sequence alignments can be edited interactively and coloured using predefined or user-supplied colouring schemes. The screenshot shows colouring according to hydrophobicity.

Grid objects (density maps, Grid maps, molecular surfaces etc.) can be cropped using an interactive tool. Bodil can display opaque and semitransparent molecular surfaces.

Installtion for Windows:
Uncompress the zipped package. That should create a folder 'bodil081'. Move that folder to "C:\Program Files".

You can make a shortcut to the bodil080\bin\bodil.bat script. It is advisable to change the 'Start in' folder for the shortcut as well as to select 'Minimized' for the 'Run' property of the shortcut.

Configurable settings in Bodil are obtained from config-files. Architecture-dependent settings override all other settings and are in common directory. User settings override global settings. The user config-files must be placed in user's own directory (usually ~/.Bodil). The name of the file(s) is not important as long as they have the extension .conf. The file can have comment lines, which start with # and empty lines. Each section starts with the section name in brackets [sectionname]. Each section has one or more settings. Each setting is in its own line, starting with key, some whitespace, equal sign (=), some whitespace, and value.

The license of this software is Freeware, you can free download and free use this calculator software.