Difference between revisions of "User:EricMartz"
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| − | I am the main author of [http:// | + | Contact: '''emartz AT microbio DOT umass DOT edu''' |
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| + | ==Projects== | ||
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| + | ===FirstGlance in Jmol=== | ||
| + | I am the main author of [http://firstglance.jmol.org FirstGlance in Jmol], a simple, browser-based tool for molecular visualization adopted by ''[http://www.nature.com/nature Nature]'', among [http://firstglance.jmol.org/adoption.htm others]. FirstGlance is designed to be useful both to novices and to specialists. It works in all popular browsers. 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. | 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. | ||
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| − | http://www. | + | ===Proteopedia.Org=== |
| + | Proteopedia, a wiki using Jmol, was created by [http://www.proteopedia.org/wiki/index.php/Proteopedia:Team Jaime Prilusky, Eran Hodis, and Joel Sussman]. Subsequently, I enthusiastically joined the project. | ||
| + | * [http://Proteopedia.Org Proteopedia.Org] | ||
| + | * [http://www.proteopedia.org/wiki/index.php/User:Eric_Martz My User Page at Proteopedia] | ||
| + | |||
| + | ===MolviZ.Org=== | ||
| + | I am the main author of [http://molviz.org MolviZ.Org] featuring molecular structure tutorials. Beginning in July, 2007, it includes Jmol-based tutorials on DNA Structure, Hemoglobin, Lipid Bilayers and Channels, and Collagen (more coming soon). It also has descriptions and links to all of my molecular visualization websites, including all the other items on this page. | ||
| − | + | ===ConSurf=== | |
| + | I am a co-author for visualization at the [http://consurf.tau.ac.il 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 [http://firstglance.jmol.org FirstGlance in Jmol]. Previously (since it went into service in 2002) ConSurf's only visualization option was [http://proteinexplorer.org Protein Explorer]. | ||
| − | + | ===Atlas of Macromolecules=== | |
| + | I am the author of an [http://atlas.proteinexplorer.org Atlas of Macromolecules], a component of [http://proteinexplorer.org Protein Explorer] (PE). In May, 2007, I upgraded the Atlas so that every entry can be visualized with [http://firstglance.jmol.org FirstGlance in Jmol] as well as with PE. | ||
| − | + | ===Protein Explorer=== | |
| − | + | I am the main author of '''[http://proteinexplorer.org ProteinExplorer.Org] (PE)''', which was built upon [http://www.proteopedia.org/wiki/index.php/Chime MDL '''Chime'''] beginning in 1998. In early June, 2005, I released a new version that exports molecular views in '''Jmol''', but this mechanism no longer works. Luckily, Bob Hanson has ported much of PE to utilize Jmol instead of Chime: [http://jmol.proteinexplorer.org Jmol.ProteinExplorer.Org]. | |
| + | |||
| + | ==Other Websites== | ||
Websites not mentioned above: | Websites not mentioned above: | ||
* [http://www.umass.edu/molvis/martz Personal Website] | * [http://www.umass.edu/molvis/martz Personal Website] | ||
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* [http://www.molvisindex.org MolVisIndex.Org]: World Index of Molecular Visualization Resources (please enter jmol websites here!) | * [http://www.molvisindex.org MolVisIndex.Org]: World Index of Molecular Visualization Resources (please enter jmol websites here!) | ||
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* [http://bioinformatics.org/mailman/listinfo/molvis-list molvis-list]: Molecular visualization email list. | * [http://bioinformatics.org/mailman/listinfo/molvis-list molvis-list]: Molecular visualization email list. | ||
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* [http://www.pdblite.org PDBLite.Org]: Simple search for macromolecular structure data (PDB files). | * [http://www.pdblite.org PDBLite.Org]: Simple search for macromolecular structure data (PDB files). | ||
Latest revision as of 20:13, 31 July 2014
Contact: emartz AT microbio DOT umass DOT edu
Contents
Projects
FirstGlance in Jmol
I am the main author of FirstGlance in Jmol, a simple, browser-based tool for molecular visualization adopted by Nature, among others. FirstGlance is designed to be useful both to novices and to specialists. It works in all popular browsers. 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.
Proteopedia.Org
Proteopedia, a wiki using Jmol, was created by Jaime Prilusky, Eran Hodis, and Joel Sussman. Subsequently, I enthusiastically joined the project.
MolviZ.Org
I am the main author of MolviZ.Org featuring molecular structure tutorials. Beginning in July, 2007, it includes Jmol-based tutorials on DNA Structure, Hemoglobin, Lipid Bilayers and Channels, and Collagen (more coming soon). It also has descriptions and links to all of my molecular visualization websites, including all the other items on this page.
ConSurf
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.
Atlas of Macromolecules
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.
Protein Explorer
I am the main author of ProteinExplorer.Org (PE), which was built upon MDL Chime beginning in 1998. In early June, 2005, I released a new version that exports molecular views in Jmol, but this mechanism no longer works. Luckily, Bob Hanson has ported much of PE to utilize Jmol instead of Chime: Jmol.ProteinExplorer.Org.
Other Websites
Websites not mentioned above:
- Personal Website
- 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).
