Protein Explorer: Difference between revisions

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Protein Explorer (formerly at ProteinExplorer.Org])<ref>Protein Explorer: Easy Yet Powerful Macromolecular Visualization. Eric Martz. ''Trends in Biochemical Sciences'', '''27''' (February):107-109, 2002.</ref> was a free macromolecular visualization software package, written largely by [[User:Eric Martz|Eric Martz]] from 1998-2006, that worked in the Firefox web browser. It was designed for students and educators, but because of its power and ease of use, was also widely used by researchers. In 2003, it won the [http://about.merlot.org/MERLOTAwards/2003awards.html Merlot Classic Award] for Exemplary Learning Materials in Biology: "Protein Explorer has revolutionized the teaching of biology at a molecular level.".

Protein Explorer utilized 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 was not open-source, and had very little development in the early 2000s. There was never a Chime for Mac OS X, and even on Windows, getting Chime to work was occasionally 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 began declining about 2005, and its development ceased in 2007.

Protein Explorer utilized the [http://www.umass.edu/microbio/chime/abtchime.htm MDL Chime] browser plugin (which did the interactive molecular rendering, much as the Jmol applet does in Proteopedia). Although free, Chime was not open-source, and had very little development in the early 2000s. There was never a Chime for Mac OS X, and even on Windows, getting Chime to work was occasionally problematic. Protein Explorer worked fully only in the [http://getfirefox.com Firefox] web browser and only in Windows. Because of these problems, and because one needed to download and install the Chime plugin in order to use it, Protein Explorer's use began declining about 2005, and its development ceased in 2007.

Protein Explorer was, at least in part, re-designed to use open-source [http://jmol.org Jmol] by [http://www.stolaf.edu/people/hansonr/ Bob Hanson] (the major developer of Jmol in recent years). This version is available at [http://jmol.proteinexplorer.org Jmol.ProteinExplorer.Org].

Protein Explorer was, at least in part, re-designed to use open-source [http://jmol.org Jmol] by [http://www.stolaf.edu/people/hansonr/ Bob Hanson] (the major developer of Jmol in recent years). This version is available at ???.

Although Protein Explorer (Chime version) was somewhat fussy to get working, it had some powerful capabilities, unmatched in ease of use, that ~~make~~ it worth the effort for some projects.

Although Protein Explorer (Chime version) was somewhat fussy to get working, it had some powerful capabilities, unmatched in ease of use, that made it worth the effort for some projects.

* Flash movies introduced how to use Protein Explorer, and a ''One-Hour Tour'' ~~gets~~ you started.

* Flash movies introduced how to use Protein Explorer, and a ''One-Hour Tour'' was available to get you started.

* It had extensive help for beginners, as well as introductory information on protein structure topics useful to researchers. No other molecular visualization program had so much built-in information about the principles of macromolecular structure. This included an extensive [http://help.proteinexplorer.org Help/Index/Glossary].

* It did nearly everything you ~~can~~ do in [[FirstGlance in Jmol]], but with greater flexibility, including identifying non-covalent interactions to any moiety (''Contacts''), and displaying salt bridges and cation-pi interactions. With the greater flexibility comes greater complexity, so [[FirstGlance in Jmol]] is even simpler to use.

* It did nearly everything you could do in [[FirstGlance in Jmol]] around 2016, but with greater flexibility, including identifying non-covalent interactions to any moiety (''Contacts''), and displaying salt bridges and cation-pi interactions. With the greater flexibility comes greater complexity, so [[FirstGlance in Jmol]] is even simpler to use. (More recently, FirstGlance has been enhanced with capabilities that Protein Explorer never had.)

* Protein Explorer enabled you to customize the display and coloring in a molecular view, just as do Proteopedia's ''Scene Authoring Tools''. In contrast, [[FirstGlance in Jmol]] limits you largely to "canned" views.

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@@ Line 1: / Line 1: @@
 Protein Explorer (formerly at ProteinExplorer.Org])<ref>Protein Explorer: Easy Yet Powerful Macromolecular Visualization. Eric Martz. ''Trends in Biochemical Sciences'', '''27''' (February):107-109, 2002.</ref> was a free macromolecular visualization software package, written largely by [[User:Eric Martz|Eric Martz]] from 1998-2006,  that worked in the Firefox web browser. It was designed for students and educators, but because of its power and ease of use, was also widely used by researchers. In 2003, it won the [http://about.merlot.org/MERLOTAwards/2003awards.html Merlot Classic Award] for Exemplary Learning Materials in Biology: "Protein Explorer has revolutionized the teaching of biology at a molecular level.".
-Protein Explorer utilized 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 was not open-source, and had very little development in the early 2000s. There was never a Chime  for Mac OS X, and even on Windows, getting Chime to work was occasionally 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 began declining about 2005, and its development ceased in 2007.
+Protein Explorer utilized the [http://www.umass.edu/microbio/chime/abtchime.htm MDL Chime] browser plugin (which did the interactive molecular rendering, much as the Jmol applet does in Proteopedia). Although free, Chime was not open-source, and had very little development in the early 2000s. There was never a Chime  for Mac OS X, and even on Windows, getting Chime to work was occasionally problematic. Protein Explorer worked fully only in the [http://getfirefox.com Firefox] web browser and only in Windows. Because of these problems, and because one needed to download and install the Chime plugin in order to use it, Protein Explorer's use began declining about 2005, and its development ceased in 2007.
-Protein Explorer was, at least in part, re-designed to use open-source [http://jmol.org Jmol] by [http://www.stolaf.edu/people/hansonr/ Bob Hanson] (the major developer of Jmol in recent years). This version is available at [http://jmol.proteinexplorer.org Jmol.ProteinExplorer.Org].
+Protein Explorer was, at least in part, re-designed to use open-source [http://jmol.org Jmol] by [http://www.stolaf.edu/people/hansonr/ Bob Hanson] (the major developer of Jmol in recent years). This version is available at ???<!--[http://jmol.proteinexplorer.org Jmol.ProteinExplorer.Org]-->.
-Although Protein Explorer (Chime version) was somewhat fussy to get working, it had some powerful capabilities, unmatched in ease of use, that make it worth the effort for some projects.
+Although Protein Explorer (Chime version) was somewhat fussy to get working, it had some powerful capabilities, unmatched in ease of use, that made it worth the effort for some projects.
-* Flash movies introduced how to use Protein Explorer, and a ''One-Hour Tour'' gets you started.
+* Flash movies introduced how to use Protein Explorer, and a ''One-Hour Tour'' was available to get you started.
 * It had extensive help for beginners, as well as introductory information on protein structure topics useful to researchers. No other molecular visualization program had so much built-in information about the principles of macromolecular structure. This included an extensive [http://help.proteinexplorer.org Help/Index/Glossary].
-* It did nearly everything you can do in [[FirstGlance in Jmol]], but with greater flexibility, including identifying non-covalent interactions to any moiety (''Contacts''), and displaying salt bridges and cation-pi interactions. With the greater flexibility comes greater complexity, so [[FirstGlance in Jmol]] is even simpler to use.
+* It did nearly everything you could do in [[FirstGlance in Jmol]] around 2016, but with greater flexibility, including identifying non-covalent interactions to any moiety (''Contacts''), and displaying salt bridges and cation-pi interactions. With the greater flexibility comes greater complexity, so [[FirstGlance in Jmol]] is even simpler to use. (More recently, FirstGlance has been enhanced with capabilities that Protein Explorer never had.)
 * Protein Explorer enabled you to customize the display and coloring in a molecular view, just as do Proteopedia's ''Scene Authoring Tools''. In contrast, [[FirstGlance in Jmol]] limits you largely to "canned" views.