From emartz at microbio.umass.edu Tue Jun 16 16:55:16 2015 From: emartz at microbio.umass.edu (Eric Martz) Date: Tue, 16 Jun 2015 16:55:16 -0400 Subject: [Molvis-list] FirstGlance in Jmol 2.3 released Message-ID: <55808D34.5030301@microbio.umass.edu> FirstGlance in Jmol version 2.3 has been released today (FirstGlance.Jmol.Org ). FirstGlance in Jmol is an easy-to-use yet powerful, free, open-source macromolecular visualization package. New structures published in /Nature/ (and several /Nature/ specialty journals) can be explored in FirstGlance by clicking the [3D] buttons in online articles. FirstGlance is offered by a number of value-added servers, including ConSurf , ExPASy , Orientations of Proteins in Membranes , and Proteopedia.Org . For example, 3v6t is a DNA-binding TAL (transcription activator-like) effector protein from phytopathogenic bacteria bound to DNA*. In addition to showing the main structural features, FirstGlance immediately alerts you to the 20 missing residues and 3 residues with incomplete sidechains, as well as rating its Rfree as "better than average at this resolution". View 3v6t in FirstGlance in Jmol . In its initial view, FirstGlance indicates missing residues and missing sidechains as well as giving each chain of the asymmetric unit a distinct color, and showing ligands with spacefilling atoms. It interprets Rfree using average and outlying values at the same resolution in the PDB. It lists ligand full names and counts and indicates their locations in one click. It offers biological unit quaternary structures through the MakeMultimer server. Any moiety of interest can be isolated in a single click (hiding the remainder of the model). Disulfide bonds, salt bridges, and cation-pi interactions are shown with a few clicks. Sequence numbers or motifs are easily found. The asymmetric unit is decorated with all crystal contacts in a single click, and easily colored by B-factor/temperature. Non-covalent interactions to any moiety are easily visualized, and divided into seven categories. FirstGlance in Jmol runs in all popular browsers in Windows, OS X and linux. It does not need Java, but will perform better with Java should you wish to install it. New in version 2.3: - All residues can be labeled with their sequence numbers and residue names. - A practical guide to homology modeling. Homology models can be uploaded to FirstGlance. - An index to help you find where a view or tool can be found, or how to see something of interest. Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- Martz.MolviZ.Org * Top Five 3D MolVis Tools: Top5.MolviZ.Org * FirstGlance: 3D Molecules in /Nature/: FirstGlance.Jmol.Org * Protein 3D Structure Wiki: Proteopedia.Org * Education: Biochem in 3D at MolviZ.Org * Find Functional Patches in Proteins: ConSurf * Atlas of Macromolecules: Atlas.MolviZ.Org * Interactive Molecules in Architectural Spaces: MolecularPlayground.Org * Workshops: Workshops.MolviZ.Org *Thanks to David Goodsell's Molecule of the Month !