User:EricMartz
I am the main author of FirstGlance in Jmol, a simple, browser-based tool for molecular visualization. FirstGlance is designed to be useful both to novices and to specialists. It works in all popular browsers and platforms, including Internet Explorer or Firefox on Windows, Safari on Mac OSX, and Mozilla Firefox on linux. A hyperlink to FirstGlance can show any PDB file in one click. It is free for all users, and its source code is freely available for others to adapt.
Key views are shown via one-click links from an always-visible control panel: secondary structure, amino and carboxy termini, general composition, hydrophobic vs. polar regions (or cores, using slab mode), charges, and multiple models when present (NMR). Convenience buttons show or hide ligands or water, toggle slab mode, zoom up/down, and change the background color. Help about each view or operation, including color keys, appears automatically, and is always in view.
I am a co-author for visualization at the ConSurf Server, which automatically colors amino acids in a 3D protein structure by evolutionary conservation. ConSurf is a project of Nir Ben-Tal and coworkers at Tel-Aviv University, Israel. In August, 2006, we enabled ConSurf to display its results in FirstGlance in Jmol. Previously (since it went into service in 2002) ConSurf's only visualization option was Protein Explorer.
I am the author of an Atlas of Macromolecules, a component of Protein Explorer (PE). In May, 2007, I upgraded the Atlas so that every entry can be visualized with FirstGlance in Jmol as well as with PE.
I am the main author of ProteinExplorer.Org (PE), which is built upon MDL Chime. In early June, 2005, I released a new version that exports molecular views in Jmol. PE's Jmol export mechanism uses Chime command scripts (recorded in PE by javascript developed by TimDriscoll) to produce jmol views as close as possible to the Chime views.
http://www.umass.edu/microbio/chime/pe_beta/my_molecules/molslides/bundled/sulfur_cage_200.jpg The exported molecular views may be accompanied by text entered into HTML forms and shown as slides to illustrate a talk. Examples are at MolSlides.Org.
PE has the capability to export slides with two adjacent molecular views, intended to be the same, one in Chime, and one in Jmol. This is provided to help identify Chime commands that do not yet work in Jmol. Volunteers to help identify these commands are welcome. Just go to ProteinExplorer.Org, generate some views, save them as MolSlides, and export them to both Chime and Jmol.
In the future, I hope to port PE itself to use Jmol instead of Chime, but that will be a large project!
Contact: emartz AT microbio DOT umass DOT edu
Websites not mentioned above:
- Personal Website
- MolviZ.Org: Educational Resources in Molecular Visualization.
- MolVisIndex.Org: World Index of Molecular Visualization Resources (please enter jmol websites here!)
- molvis-list: Molecular visualization email list.
- PDBLite.Org: Simple search for macromolecular structure data (PDB files).
