FirstGlance in Jmol: Difference between revisions
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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 the free open-source [[Jmol|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 ([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 the free open-source [[Jmol|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. | ||
''3D View'' or "3D" links to FirstGlance in Jmol have been available in every article reporting a new structure in [http://www.nature.com/nsmb ''Nature Structural and Molecular Biology''] beginning in February, 2006, and in [http://www.nature.com/nature ''Nature''] from November, 2007. It is also offered as a visualization option by numerous structural bioinformatics servers and databases, including '''Proteopedia''', [[Conservation, Evolutionary|ConSurf]], the [[Protein Data Bank]], [http://opm.phar.umich.edu/ Orientations of Proteins in Membranes], and [http://firstglance.jmol.org/adoption.htm others]. | ''3D View'' or "3D" links to FirstGlance in Jmol have been available in every article reporting a new structure in [http://www.nature.com/nsmb ''Nature Structural and Molecular Biology''] beginning in February, 2006, and in [http://www.nature.com/nature ''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 ''[http://proteinscience.org/ Protein Science]'', '''Proteopedia''', [[Conservation, Evolutionary|ConSurf]], the [[Protein Data Bank]], [http://opm.phar.umich.edu/ Orientations of Proteins in Membranes], and [http://firstglance.jmol.org/adoption.htm 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. | 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. | ||