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 free open-source Jmol, as does Proteopedia. It works in the most popular web browsers, and MS Windows, Apple Mac OS X, and linux. It operates from menus and forms -- no familiarity with the Jmol command scripting language is required. Tooltips are used extensively, and explanatory help, with color keys, appears automatically for each view.
In order to be as easy as possible to use, FirstGlance in Jmol does not provide tools to customize 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.
Non-covalent interactions (hydrogen bonds, salt bridges, hydrophobic interactions) with any designated target moiety are displayed automatically in a powerful Contacts dialog in FirstGlance in Jmol. The target moiety (a chain, a range of residues in a chain, a residue or group, or a single atom) is selected beforehand by clicking on it.
Any molecular view obtained in FirstGlance in Jmol can become a scene attached to a green link in Proteopedia: please see Help:Copying FirstGlance Scenes into Proteopedia.
Following the example set by Proteopedia in early 2014, beginning with FirstGlance version 2.00 (released late April, 2014), FirstGlance in Jmol works without Java by default (see four forms of Jmol). Optionally, there is a preference setting to use the signed Jmol Java applet by default.
3D View or "3D" 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 from November, 2007. It is also offered as a visualization option by other journals and numerous structural bioinformatics servers and databases, including the journal Protein Science, several other Nature "spinoff" journals, Proteopedia, ConSurf, the Protein Data Bank, Orientations of Proteins in Membranes, and others.