Protein Explorer: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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-Protein Explorer ([http://proteinexplorer.org ProteinExplorer.Org]) is a free macromolecular visualization software package, written largely by [[User:Eric Martz|Eric Martz]] from 1998-2006,  that works in the Firefox web browser. Protein Explorer utilizes the [http://www.umass.edu/microbio/chime/abtchime.htm MDL Chime] browser plugin (which does the interactive molecular rendering, much as the Jmol applet does in Proteopedia). Although free, Chime is not open-source, and has had very little development in recent years. There is no Chime available for Mac OS X, and even on Windows, getting Chime to work can sometimes be problematic. Protein Explorer works fully only in the [http://getfirefox.com Firefox] web browser and only in Windows. Because of these problems, and because one must download and install the Chime plugin in order to use it, Protein Explorer's use has been declining since about 2005.
+Protein Explorer ([http://proteinexplorer.org ProteinExplorer.Org]) is a free macromolecular visualization software package, written largely by [[User:Eric Martz|Eric Martz]] from 1998-2006,  that works in the Firefox web browser. Protein Explorer utilizes the [http://www.umass.edu/microbio/chime/abtchime.htm MDL Chime] browser plugin (which does the interactive molecular rendering, much as the Jmol applet does in Proteopedia). Although free, Chime is not open-source, and has had very little development in recent years. There is no Chime available for Mac OS X, and even on Windows, getting Chime to work can occasionally be problematic. Protein Explorer works fully only in the [http://getfirefox.com Firefox] web browser and only in Windows. Because of these problems, and because one must download and install the Chime plugin in order to use it, Protein Explorer's use has been declining since about 2005.
 Protein Explorer could be re-designed to use open-source [http://jmol.org Jmol], but this is a large undertaking. [http://www.stolaf.edu/people/hansonr/ Bob Hanson] (the major developer of Jmol in recent years) has begun this re-design, but in October 2008, his Jmol version of Protein Explorer is far from being fully operational.
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 Although Protein Explorer is somewhat fussy to get working, it has some powerful capabilities, unmatched in ease of use, that make it worth the effort for some projects.
-# Its NMR/Animation control panel facilitates exploration and animation of multiple-model PDB files, with great flexibility and control. It generates an animation script, from menus and buttons, that runs in both Chime and RasMol. Running this script in RasMol saves each frame as a .gif snapshot file, and these can then be assembled into a multi-gif movie. [http://proteinexplorer.org/morfdoc.htm Examples].
+* It has extensive help for beginners, as well as introductory information on protein structure topics useful to researchers. No other molecular visualization program has so much built-in assistance. This includes an extensive [[http://help.proteinexplorer.org Help/Index/Glossary]].
+* It can be downloaded and used off-line.
+* Its NMR/Animation control panel facilitates exploration and animation of multiple-model PDB files, with great flexibility and control. It generates an animation script, from menus and buttons, that runs in both Chime and RasMol. Running this script in RasMol saves each frame as a .gif snapshot file, and these can then be assembled into a multi-gif movie. [http://proteinexplorer.org/morfdoc.htm Examples].