Difference between revisions of "User:EricMartz"

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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/nsmb Nature Structural and Molecular Biology]'', 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 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.
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Contact: '''emartz AT microbio DOT umass DOT edu'''
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==Projects==
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===FirstGlance in Jmol===
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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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===Proteopedia.Org===
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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.
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* [http://Proteopedia.Org Proteopedia.Org]
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* [http://www.proteopedia.org/wiki/index.php/User:Eric_Martz My User Page at Proteopedia]
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===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.
 
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.
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===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].
 
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].
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===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.  
 
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.  
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I am the main author of '''[http://proteinexplorer.org 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.
 
  
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The exported molecular views may be accompanied by text entered into HTML forms and shown as slides to illustrate a talk. Examples are at [http://molslides.org MolSlides.Org].
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===Protein Explorer===
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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].
  
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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.
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==Other Websites==
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In the future, I hope to port PE itself to use Jmol instead of Chime, but that will be a large project!
 
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Contact: '''emartz AT microbio DOT umass DOT edu'''
 
  
 
Websites not mentioned above:
 
Websites not mentioned above:

Latest revision as of 20:13, 31 July 2014

Contact: emartz AT microbio DOT umass DOT edu

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:

Contributors

EricMartz, NicolasVervelle

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