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| DS Visualizer | BALLView | VMD | RasMol | MOLMOL | Chimera |
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Li Liu
The Lindsay Lab at Arizona State University
Last modified: July 12, 2007
Overview
Stand-alone Applications
(6)
Easy view and explore
with web browser (3)
Overview
This site brings together some of the best software for visualizing macromolecular structures. You are welcome to use the image and animation files we created using these tools. Feel free to contact us with any questions and comments.
There has been a long tradition of creating physical models to demonstrate properties of molecules. One goal of mainstream molecular graphics has been to represent the "ball and stick" physical model as realistically as possible and to couple this with calculations of molecular properties. Graphics can also be animated to represent molecular processes and chemical reactions, a feat that is not easy to reproduce physically.
All software listed here can read standard Protein Data Bank (PDB) files and display the contained structure. PDB is a repository for 3-D structural data of proteins and nucleic acids. This data, typically obtained by X-ray crystallography or NMR spectroscopy, is submitted by biologists and biochemists from around the world, and can be accessed for free. The database contains over 44000 structures as of July 2007.
Stand-alone applications
DSVisualizer
| BALLView | VMD | RasMol | MOLMOL | Chimera
Discovery Studio Visualizer
Discovery Studio Visualizer is a product of Accelrys Software Inc. It is free to all researchers
Click
here for our image gallery created with DS Visualizer.
Summary: A commercial-grade graphics visualization tool for small molecules and macromolecules. A molecule can be viewed as a wireframe, a stick model, a ball and stick model, or a space-filling model. Distances, angles, torsions, and stereochemistry can be measured. Molecules drawn in 2D in ISIS/Draw or ChemDraw can be converted to the proper 3D geometry automatically.
Latest release:Discovery Studio 1.7 (2006)
BALLView
Ball View is currently maintained by Center for Bioinformatics Saarbrücken & Center for Bioinformatics Tübingen, Germany
Click
here for our image gallery created with BALLView.
Summary: In addition to visualizing and modeling bio-molecular structures, BALLView also offers functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER and CHARMM force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, and secondary structure calculation. Results of these computations can be exported as images or as movies.
Latest release:BALL 1.1.1 (2005)
VMD
VMD (Visual Molecular Dynamics) was developed by The Theoretical and Computational Biophysics Group at UIUC
Click
here for our image gallery created with VMD.
Summary: 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. It can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation.
Latest release:VMD 1.8.5 (2006)
RasMol
RasMol is an open source program created by Roger Sayle in 1992.
Click
here for our image gallery created with RasMol.
Summary: RasMol is aimed at display, teaching and generation of publication quality images. RasMol can read a prepared list of commands from a script file to allow a given image or viewpoint to be restored quickly. RasMol can also create a script file containing the commands required to regenerate the current image.
Latest release:RasMol 2.7.3 (2005) Quick Reference: RasMol
MOLMOL
MOLMOL was part of a collaboration project between BRUKER/Spectrospin and Prof. Wüthrich at ETH Zürich
Click
here for our image gallery created with MOLMOL.
Summary: MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of molecules, with special emphasis on biological macromolecules. The program has features that make it particularly useful for the study of protein or DNA structures determined by NMR. MOLMOL has about 260 commands that can be entered on the command line. Parts of commands that are unique are completed automatically while typing..
Latest release:MOLMOL 2K.2 (2003) Quick Reference: MOLMOL
Chimera
Chimera is developed and supported by the UCSF Resource for Biocomputing, Visualization, and Informatics and is funded by the NIH.
Click
here for our image gallery created with Chimera.
Summary: Generates high-quality images and animations suitable for publication and presentation. Provides tools to show density maps and analyze microscopy data; utilize symmetry information for the display of higher-order structures; display multiple sequence alignments, with crosstalk between the sequences and structures; and enable analysis of molecular dynamics trajectories and docking results.
Latest release: Chimera 1.2304 (2006)
View and explore with web browser
FirstGlance in
Jmol | Protein Explorer | The ConSurf server
FirstGlance in Jmol
FirstGlance in Jmol is developed and maintained by the group of Prof. Eric Martz, University of Massachusetts
Summary: FirstGlance in Jmol was designed to enable the readers of scientific journals to see the main features of newly published 3D models (PDB file) in a few clicks. It displays major structural features of the molecule, including secondary structure, ribbons, amino to carboxy (or 5' to 3') rainbow, Composition, Hydrophobic/Polar, Charge, Vines, Salt Bridges and Cation-Pi Orbital Interactions.
Protein Explorer
Protein Explorer is developed and maintained by the group of Prof. Eric Martz, University of Massachusetts
Summary: Protein Explorer is for visualizing the 3D structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. It is suitable for high school and college students, yet it is also widely used by graduate students and researchers. Protein Explorer understands RasMol commands. Required installation: MDL Chime browser plugin.
The ConSurf server
Summary: The ConSurf server identifies functionally important regions on the surface of a protein by coloring each amino acid in a protein chain according to its level of evolutionary conservation. User provides a PDB code and a chain name.
