FirstGlance in Jmol

FirstGlance in Jmol (firstglance.jmol.org) is a free, open-source, macromolecular visualization software package that operates on-line in a web browser. It uses the free open-source Jmol java applet, as does Proteopedia. It works in the most popular web browsers, and MS Windows, Apple Mac OS X, and linux.

FirstGlance in Jmol was designed to provide interactive visualization of macromolecular structures reported in published journal articles. Thus, it assumes that you know the name of the molecule, and something about it, beforehand. 3D View links to FirstGlance in Jmol have been available in every article reporting a new structure in Nature Structural and Molecular Biology beginning in February, 2006, and in Nature beginning in November, 2007. It is also offered as a visualization option by numerous structural bioinformatics servers and databases, including Proteopedia, ConSurf, the Protein Data Bank, Orientations of Proteins in Membranes, and others.

In order to be as easy as possible to use, FirstGlance in Jmol does not offer much customization of the molecular view, but rather offers a series of "canned" views that reveal the major structural features of the molecule, such as composition (protein, DNA, RNA, ligand and solvent) secondary structure, amino and carboxy termini, hydrophobic and polar surfaces, surface charges, salt bridges and cation-pi interactions. Any moiety can be hidden by clicking on it in Hide mode. Any residue or sequence number can be found/located in the Find dialog.

(to be continued ... Eric Martz 20:46, 18 October 2008 (IST))