FirstGlance in Jmol: Difference between revisions
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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]]). | 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 in Jmol ([http://firstglance.jmol.org firstglance.jmol.org]) is a free, open-source, macromolecular visualization software package that operates on-line in a web browser. It uses | FirstGlance in Jmol ([http://firstglance.jmol.org 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. | 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. | ||