Molecular modeling and visualization software

Visualization vs. ModelingVisualization vs. Modeling

Software for visualizing the three-dimensional structures of molecules, molecular visualization software, can be distinguished from molecular modeling software. Strictly speaking, Visualization software displays a pre-existing molecular model without changing it, while modeling software can create the model, or modify it by adding or removing moieties, changing covalent bonds, bond angles, conformation, or non-covalent interactions.

Free molecular visualization softwareFree molecular visualization software

Examples of popular free molecular visualization software packages include:

• Jmol, an open-source java-based program available in stand-alone or applet forms. The applet is used in Proteopedia, and in the free educational software Molecular Workbench. Effective use of Jmol requires learning a command scripting language.
• FirstGlance in Jmol, an open-source user-interface to Jmol utilized for a decade in the 3D View links in papers in the journal Nature that report new macromolecular structures. Proteopedia's automatically seeded pages (pages titled with a PDB code) have links for further exploration of the structure in FirstGlance in Jmol. Although FirstGlance in Jmol by no means exploits all the power in Jmol, it does show the main structural features of a macromolecule without learning any command scripting language. More ...
• ChimeraX (free for non-commercial use only).
• iCn3D, a powerful menu and command driven package from the US National Center for Biotechnology Information.
• Mol* (MolStar) is offered as a visualization option by the wwPDB. Its rendering is fast and smooth because it uses WebGL, and it can handle very large numbers of atoms.
• NGL Viewer is offered as a visualization option by the wwPDB. Its rendering is fast and smooth because it uses WebGL.
• Samson, a powerful visualization and modeling package that is menu-driven. Free for basic use. See demos at Sculpting protein conformations and the step-by-step demo at tinyurl.com/sculpting-proteins.
• Kinemages, Mage and KiNG (KiNG = Kinemage, Next Generation) are designed to present the author's viewpoint of a molecular structure. They excel in specialized areas, but are not optimal for general purpose visualization. KiNG can be used in Proteopedia; an example may be seen at Hemoglobin#Hemoglobin_subunit_binding_O2.
• RasMol, an open-source stand-alone program released in 1993, and still popular. Effective use of RasMol requires learning a command scripting language.
• Protein Explorer, an extensive and powerful open-source user-interface to Chime. Although there is nothing else available in 2009 that combines the power and ease of use of Protein Explorer, it is falling into disuse because of difficulties related to installation and operation of the Chime browser plugin. Because Jmol is now much more powerful and easier to get working, especially on OS X, maintenance of Protein Explorer ceased in 2007. A start has been made at implementing Protein Explorer with Jmol, but this project is in its infancy. (Volunteers are needed!)
• Chime, a free browser plugin released in 1996, now superceded by Jmol. Not open-source.
• ICM-Browser and the free plugi-in ActiveICM both by Molsoft are now used to view enhanced content in Molecular and Cellular Proteomics Journal and PLoS (Public Library of Science) series of journals, such as an example is enhanced version that is viewable in a browser and this example article with separate Datapack. Requires a download and/or plugin. Not open-source.
• HOLLOW is not a stand-alone molecular visualization program; however, it facilitates the production of surface images of proteins. You input a PDB file and get out a PDB file of dummy water atoms that forms a "cast" of the voids and channels of a protein.
• RINalyzer enables analyzing and visualizing residue interaction networks (RINs) constructed from the three-dimensional structure of a protein as stored in PDB files from the Protein Data Bank. RINalyzer allows simultaneous, interactive 2D visualization and exploration of a RIN in Cytoscape, in conjunction with the molecular 3D structure visualized in the UCSF Chimera visulization/modelling system. Cytoscape is a free, open-source software platform for the analysis and visualization of molecular interaction networks. RIN Data for any PDB entry can be downloaded here using the PDB code, alternatively the RING web server can be used to generate RINs.
• Qutemol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol produces images in real time by running algorithms that rely on modern graphic card features, including programmable fragment & vertex shaders, and frame and vertex buffer objects. Other molecular visualization software has also been developed to take advantage of the current generation of high powered video graphic cards or graphic processing units (GPUs), see Chavent et al. 2011. GPU-powered tools boost molecular visualization..
• iView - an interactive WebGL visualizer of protein-ligand complexes
• PV - JavaScript Protein Viewer

Free molecular modeling softwareFree molecular modeling software

Molecular modeling software usually includes visualization capabilities.

• Swiss-PDBViewer = DeepView, a powerful and popular free modeling package (not open-source). Although menu-driven, there is a significant learning curve.
• Coot (Crystallographic Object-Oriented Toolkit -- also at Google Code), is very popular among crystallographers for building macromolecular models from electron density maps. Open source (GNU GPL).
• CCP4 (Collaborative Computational Project No. 4: Software for Macromolecular X-Ray Crystallography) is very popular with crystallographers. Free for non-commercial use.
• O has long been popular with crystallographers for building macromolecular models from electron density maps. Free. (License unclear.)
• Modeller
• UCSF Chimera
• TINKER a free molecular modeling package for molecular mechanics and dynamics, with some special features for biopolymers.
• Abalone a program focused on molecular dynamics of biopolymers.
• GPCR-ModSim is a webserver for computational modeling and simulation of G-Protein Coupled Receptors (GPCRs). Models from sequence and also lets you place the models in a phospholipid bilayer and model them using Molecular Dynamics.

See AlsoSee Also

• Introduction to molecular visualization
• History of Macromolecular Visualization
• Homology model
• PyMOL, an open-source molecular visualization program, extremely popular with crystallographers, that requires a subscription fee. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.
• eMovie is a plugin for PyMOL that facilitates creation of true movies using a storyboard approach.
• Molecular sculpture
• Web servers for convenient generation of publication-quality figures for molecular views