First time at Proteopedia? Click on the green links: they change the 3D image. Click and drag the molecules. Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, you can edit pages in Proteopedia. Visit the Main Page to learn more.
FirstGlance in Jmol
Every molecule in Proteopedia can be explored in FirstGlance in Jmol, using the link beneath the molecule (on pages titled with a PDB code).
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. 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.
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 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.