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The program can meaure distances, angles, and torsional angles between atoms. Molecules can be superimposed and RMSD (Root Mean Square Deviation) between atom coordinates can be calculated. Additionaly, protein chains can be structurally aligned to detect regions of high structural similarity. iMol can load multimodel PDB files and display them as a dynamics trajectory.

iMol uses OpenGL graphics to display molecules. The molecules can be rendered using various styles: wires, points, Van der Waals spheres, balls and sticks, polygons, strands, ribbon, cartoons, spring, tube, ladder. Individual atoms and/or residues can be selected and rendered independly. The rendering styles can be mixed up to visualize complex molecular systems in a more convienient way. There are several predefined color schemes available (e.g. residuum order, secondary structure, hydrophobicity), as well as custom colors. Also, different materials (e.g. plastic, metal, glass) can be used. The rendered images may be exported as a bitmap, as a PostScript file, or as a POV-Ray file.

Several rendering effects are available, including automatic rotation, motion blur, depth cueing (fog), background gradient, perspective, and stereo projection (using both side-by-side and red/blue anaglyph methods). Various rendering parameters can be fine-tuned.

VMD 1.8.7 offers you a perfect and extremely useful which is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

Major Features:

1. Support for all major computer platforms
2. Support for multicore processors
3. Support for GPU accelerated computation
4. Many excellent VMD tutorials developed locally, and by the research community at large
5. No limits on the number of molecules, atoms, residues or number of trajectory frames, except available memory
6. Many molecular rendering and coloring methods
7. Stereo display capability
8. Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more)
9. Support for over 60 molecular file formats and data types through an extensive library of built-in file reader/writer plugins and translators
10. VMD includes a multiple sequence alignment plugin, a unified bioinformatics analysis environment that allows one to organize, display, and analyze both sequence and structure data for proteins and nucleic acids.
11. Ability to export displayed graphics to files which may be processed by a number of popular ray tracing and image rendering packages, including POV-Ray, Rayshade, Raster3D, and Tachyon.
12. User-extensible graphical and text-based user interfaces, built-on standard Tcl/Tk and Python scripting languages
13. Extensions to the Tcl language which enable researchers to write their own routines for molecular analysis
14. Modular, extensible source code using an object-oriented design in C++, with a programmers guide describing the program architecture and source code
15. Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD in the Theoretical and Computational Biophysics Group at the University of Illinois.
16. VMD works well with projected display systems like the 3-D Projection Facility maintained by the Theoretical and Computational Biophysics Group.
17. VMD can be used to concurrently display and interact with a running NAMD simulation.
18. Using VMD as a Web/MIME Helper Application
19. VMD script library
20. Portable and Intuitive GUI
21. Interfacing with MD Programs (i.e. SIGMA, NAMD)
22. Interactive MD and VR Device Support
23. Making Movies with VMD