FirstGlance in Jmol

From Proteopedia

Screenshot of 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, such as 1d66). FirstGlance has many unique and powerful capabilities not found in other viewers such as PyMOL, ChimeraX, or Mol* offered by the wwPDB.

When you go directly to FirstGlance in Jmol, you can enter any PDB code, or upload a PDB file from your computer, such as a prediction by AlphaFold or a homology model.

FirstGlance in Jmol provides an easy interface to make a Powerpoint-ready animation from any of its molecular views. Examples: tinyurl.com/movingmolecules. FirstGlance in Jmol version 4.0 was released August 15, 2022, with new capability to automatically construct large assemblies such as virus capsids.

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 JSmol, 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 everywhere, and explanatory help, with color keys and examples for comparison, appear 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 scene obtained in FirstGlance in Jmol can be saved, with just a few clicks, as a high-resolution static image, or as a presentation-ready animation. Examples of molecular animations made with FirstGlance, in slides.

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.

Java Not Needed

Following the example set by Proteopedia in early 2014, beginning with FirstGlance version 2.00 (released late April, 2014), FirstGlance in Jmol uses the Javascript version of Jmol, JSmol, and thus works without Java (see four forms of Jmol).

Adoptions

3D View or "3D" links to FirstGlance in Jmol were offered in every article reporting a new structure in Nature Structural and Molecular Biology from February, 2006 through December, 2018, and in Nature from November, 2007 through March, 2018. It has also been 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.

See Also

• FirstGlance/Index lists related resources within Proteopedia and elsewhere.
• Teaching with FirstGlance in Jmol.
• Help:Copying FirstGlance Scenes into Proteopedia.
• What is FirstGlance in Jmol? (Includes comparisons with other software packages.)
• All About FirstGlance in Jmol.
• Jmol
• Molecular modeling and visualization software
• Protein Explorer.