Protein Explorer - Revision history

http://52.214.119.220/wiki/index.php?action=history&feed=atom&title=Protein_Explorer Protein Explorer - Revision history 2026-04-15T03:04:11Z Revision history for this page on the wiki MediaWiki 1.11.2 http://52.214.119.220/wiki/index.php?title=Protein_Explorer&diff=3526213&oldid=prev Eric Martz at 17:49, 2 March 2022 2022-03-02T17:49:13Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 17:49, 2 March 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 11:</td> <td colspan="2" class="diff-lineno">Line 11:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* 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].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* 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].</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* It did nearly everything you <del style="color: red; font-weight: bold; text-decoration: none;">can </del>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.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* It did nearly everything you <ins style="color: red; font-weight: bold; text-decoration: none;">could </ins>do in [[FirstGlance in Jmol]] <ins style="color: red; font-weight: bold; text-decoration: none;">around 2016</ins>, 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. <ins style="color: red; font-weight: bold; text-decoration: none;">(More recently, FirstGlance has been enhanced with capabilities that Protein Explorer never had.)</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* 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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* 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.</div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=Protein_Explorer&diff=3526212&oldid=prev Eric Martz at 17:46, 2 March 2022 2022-03-02T17:46:29Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 17:46, 2 March 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 7:</td> <td colspan="2" class="diff-lineno">Line 7:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Flash movies introduced how to use Protein Explorer, and a ''One-Hour Tour'' <del style="color: red; font-weight: bold; text-decoration: none;">gets </del>you started.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* Flash movies introduced how to use Protein Explorer, and a ''One-Hour Tour'' <ins style="color: red; font-weight: bold; text-decoration: none;">was available to get </ins>you started.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* 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].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* 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].</div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=Protein_Explorer&diff=3526211&oldid=prev Eric Martz at 17:46, 2 March 2022 2022-03-02T17:46:06Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 17:46, 2 March 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 5:</td> <td colspan="2" class="diff-lineno">Line 5:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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 ???.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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 ???.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Although Protein Explorer (Chime version) was somewhat fussy to get working, it had some powerful capabilities, unmatched in ease of use, that <del style="color: red; font-weight: bold; text-decoration: none;">make </del>it worth the effort for some projects.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Although Protein Explorer (Chime version) was somewhat fussy to get working, it had some powerful capabilities, unmatched in ease of use, that <ins style="color: red; font-weight: bold; text-decoration: none;">made </ins>it worth the effort for some projects.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Flash movies introduced how to use Protein Explorer, and a ''One-Hour Tour'' gets you started.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Flash movies introduced how to use Protein Explorer, and a ''One-Hour Tour'' gets you started.</div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=Protein_Explorer&diff=3526210&oldid=prev Eric Martz at 17:45, 2 March 2022 2022-03-02T17:45:42Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 17:45, 2 March 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 3:</td> <td colspan="2" class="diff-lineno">Line 3:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>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 <ins style="color: red; font-weight: bold; text-decoration: none;">???</ins>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=Protein_Explorer&diff=3526209&oldid=prev Eric Martz at 17:44, 2 March 2022 2022-03-02T17:44:54Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 17:44, 2 March 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.".</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.".</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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 <del style="color: red; font-weight: bold; text-decoration: none;">works </del>fully only in the [http://getfirefox.com Firefox] web browser and only in Windows. Because of these problems, and because one <del style="color: red; font-weight: bold; text-decoration: none;">must </del>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.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>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 <ins style="color: red; font-weight: bold; text-decoration: none;">worked </ins>fully only in the [http://getfirefox.com Firefox] web browser and only in Windows. Because of these problems, and because one <ins style="color: red; font-weight: bold; text-decoration: none;">needed to </ins>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.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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].</div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=Protein_Explorer&diff=3526208&oldid=prev Eric Martz at 17:44, 2 March 2022 2022-03-02T17:44:10Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 17:44, 2 March 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.".</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.".</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Protein Explorer utilized the [http://www.umass.edu/microbio/chime/abtchime.htm MDL Chime] browser plugin (which <del style="color: red; font-weight: bold; text-decoration: none;">does </del>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.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Protein Explorer utilized the [http://www.umass.edu/microbio/chime/abtchime.htm MDL Chime] browser plugin (which <ins style="color: red; font-weight: bold; text-decoration: none;">did </ins>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.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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].</div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=Protein_Explorer&diff=3526207&oldid=prev Eric Martz at 17:43, 2 March 2022 2022-03-02T17:43:52Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 17:43, 2 March 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.".</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.".</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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, <del style="color: red; font-weight: bold; text-decoration: none;">'''</del>Protein Explorer's use <del style="color: red; font-weight: bold; text-decoration: none;">has been </del>declining <del style="color: red; font-weight: bold; text-decoration: none;">since </del>about 2005, and its development ceased in 2007<del style="color: red; font-weight: bold; text-decoration: none;">'''</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>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 <ins style="color: red; font-weight: bold; text-decoration: none;">began </ins>declining about 2005, and its development ceased in 2007.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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].</div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=Protein_Explorer&diff=3526206&oldid=prev Eric Martz at 17:42, 2 March 2022 2022-03-02T17:42:48Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 17:42, 2 March 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Protein Explorer (<del style="color: red; font-weight: bold; text-decoration: none;">[http://proteinexplorer.org </del>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.".</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Protein Explorer (<ins style="color: red; font-weight: bold; text-decoration: none;">formerly at </ins>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.".</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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 has been declining since about 2005, and its development ceased in 2007'''.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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 has been declining since about 2005, and its development ceased in 2007'''.</div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=Protein_Explorer&diff=3526205&oldid=prev Eric Martz at 17:42, 2 March 2022 2022-03-02T17:42:15Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 17:42, 2 March 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 3:</td> <td colspan="2" class="diff-lineno">Line 3:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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 has been declining since about 2005, and its development ceased in 2007'''.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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 has been declining since about 2005, and its development ceased in 2007'''.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Protein Explorer <del style="color: red; font-weight: bold; text-decoration: none;">has been</del>, 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].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Protein Explorer <ins style="color: red; font-weight: bold; text-decoration: none;">was</ins>, 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].</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Although Protein Explorer (Chime version) <del style="color: red; font-weight: bold; text-decoration: none;">is </del>somewhat fussy to get working, it <del style="color: red; font-weight: bold; text-decoration: none;">has </del>some powerful capabilities, unmatched in ease of use, that make it worth the effort for some projects.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Although Protein Explorer (Chime version) <ins style="color: red; font-weight: bold; text-decoration: none;">was </ins>somewhat fussy to get working, it <ins style="color: red; font-weight: bold; text-decoration: none;">had </ins>some powerful capabilities, unmatched in ease of use, that make it worth the effort for some projects.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Flash movies <del style="color: red; font-weight: bold; text-decoration: none;">introduce </del>how to use Protein Explorer, and a ''One-Hour Tour'' gets you started.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* Flash movies <ins style="color: red; font-weight: bold; text-decoration: none;">introduced </ins>how to use Protein Explorer, and a ''One-Hour Tour'' gets you started.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* It <del style="color: red; font-weight: bold; text-decoration: none;">has </del>extensive help for beginners, as well as introductory information on protein structure topics useful to researchers. No other molecular visualization program <del style="color: red; font-weight: bold; text-decoration: none;">has </del>so much built-in information about the principles of macromolecular structure. This <del style="color: red; font-weight: bold; text-decoration: none;">includes </del>an extensive [http://help.proteinexplorer.org Help/Index/Glossary].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* It <ins style="color: red; font-weight: bold; text-decoration: none;">had </ins>extensive help for beginners, as well as introductory information on protein structure topics useful to researchers. No other molecular visualization program <ins style="color: red; font-weight: bold; text-decoration: none;">had </ins>so much built-in information about the principles of macromolecular structure. This <ins style="color: red; font-weight: bold; text-decoration: none;">included </ins>an extensive [http://help.proteinexplorer.org Help/Index/Glossary].</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* It <del style="color: red; font-weight: bold; text-decoration: none;">does </del>nearly everything you can do in [[FirstGlance in Jmol]], but with greater flexibility, including identifying <del style="color: red; font-weight: bold; text-decoration: none;">noncovalent </del>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.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* It <ins style="color: red; font-weight: bold; text-decoration: none;">did </ins>nearly everything you can do in [[FirstGlance in Jmol]], but with greater flexibility, including identifying <ins style="color: red; font-weight: bold; text-decoration: none;">non-covalent </ins>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.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Protein Explorer <del style="color: red; font-weight: bold; text-decoration: none;">enables </del>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.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* Protein Explorer <ins style="color: red; font-weight: bold; text-decoration: none;">enabled </ins>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.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* It <del style="color: red; font-weight: bold; text-decoration: none;">can </del>be downloaded and used off-line.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* It <ins style="color: red; font-weight: bold; text-decoration: none;">could </ins>be downloaded and used off-line.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Protein Explorer <del style="color: red; font-weight: bold; text-decoration: none;">does </del>a better job of reformatting the information in the [[PDB file]] header into a compact yet intelligible format, and explaining the terminology involved (e.g. Resolution, R value and Rfree) than <del style="color: red; font-weight: bold; text-decoration: none;">does </del>any other macromolecular visualization package.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* Protein Explorer <ins style="color: red; font-weight: bold; text-decoration: none;">did </ins>a better job of reformatting the information in the [[PDB file]] header <ins style="color: red; font-weight: bold; text-decoration: none;">section </ins>into a compact yet intelligible format, and explaining the terminology involved (e.g. Resolution, R value and Rfree) than <ins style="color: red; font-weight: bold; text-decoration: none;">did </ins>any other macromolecular visualization package <ins style="color: red; font-weight: bold; text-decoration: none;">at the time</ins>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* A clickable sequence listing <del style="color: red; font-weight: bold; text-decoration: none;">shows where </del>any residue <del style="color: red; font-weight: bold; text-decoration: none;">is </del>in the 3D structure ("Seq3D").</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* A clickable sequence listing <ins style="color: red; font-weight: bold; text-decoration: none;">showed the location of </ins>any residue in the 3D structure ("Seq3D").</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Its NMR/Animation control panel <del style="color: red; font-weight: bold; text-decoration: none;">facilitates </del>exploration and animation of multiple-model PDB files, with great flexibility and control. It <del style="color: red; font-weight: bold; text-decoration: none;">generates </del>an animation script, from menus and buttons, that <del style="color: red; font-weight: bold; text-decoration: none;">runs </del>in both Chime and RasMol. Running this script in RasMol <del style="color: red; font-weight: bold; text-decoration: none;">saves </del>each frame as a .gif snapshot file, and these <del style="color: red; font-weight: bold; text-decoration: none;">can </del>then be assembled into a multi-gif movie. [http://proteinexplorer.org/morfdoc.htm Examples].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* Its NMR/Animation control panel <ins style="color: red; font-weight: bold; text-decoration: none;">facilitated </ins>exploration and animation of multiple-model PDB files, with great flexibility and control. It <ins style="color: red; font-weight: bold; text-decoration: none;">generated </ins>an animation script, from menus and buttons, that <ins style="color: red; font-weight: bold; text-decoration: none;">ran </ins>in both Chime and RasMol. Running this script in RasMol <ins style="color: red; font-weight: bold; text-decoration: none;">saved </ins>each frame as a .gif snapshot file, and these <ins style="color: red; font-weight: bold; text-decoration: none;">could </ins>then be assembled into a multi-gif movie. [http://proteinexplorer.org/morfdoc.htm Examples].</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Protein Explorer's MSA3D <del style="color: red; font-weight: bold; text-decoration: none;">can </del>color a 3D protein model by evolutionary conservation from a multiple-sequence alignment containing as few as two sequences. Although the [[Conservation, Evolutionary|ConSurf Server]] calculates evolutionary conservation with a greatly superior algorithm (and then colors the 3D model accordingly), it requires a minimum of five sequences.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* Protein Explorer's MSA3D <ins style="color: red; font-weight: bold; text-decoration: none;">was able to </ins>color a 3D protein model by evolutionary conservation from a multiple-sequence alignment containing as few as two sequences. Although the [[Conservation, Evolutionary|ConSurf Server]] calculates evolutionary conservation with a greatly superior algorithm (and then colors the 3D model accordingly), it requires a minimum of five sequences.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==See Also==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==See Also==</div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=Protein_Explorer&diff=3526204&oldid=prev Eric Martz at 17:37, 2 March 2022 2022-03-02T17:37:19Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 17:37, 2 March 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Protein Explorer ([http://proteinexplorer.org ProteinExplorer.Org])<ref>Protein Explorer: Easy Yet Powerful Macromolecular Visualization. Eric Martz. ''Trends in Biochemical Sciences'', '''27''' (February):107-109, 2002.</ref> <del style="color: red; font-weight: bold; text-decoration: none;">is </del>a free macromolecular visualization software package, written largely by [[User:Eric Martz|Eric Martz]] from 1998-2006, that <del style="color: red; font-weight: bold; text-decoration: none;">works </del>in the Firefox web browser. It was designed for students and educators, but because of its power and ease of use, <del style="color: red; font-weight: bold; text-decoration: none;">has </del>also <del style="color: red; font-weight: bold; text-decoration: none;">been </del>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.".</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Protein Explorer ([http://proteinexplorer.org ProteinExplorer.Org])<ref>Protein Explorer: Easy Yet Powerful Macromolecular Visualization. Eric Martz. ''Trends in Biochemical Sciences'', '''27''' (February):107-109, 2002.</ref> <ins style="color: red; font-weight: bold; text-decoration: none;">was </ins>a free macromolecular visualization software package, written largely by [[User:Eric Martz|Eric Martz]] from 1998-2006, that <ins style="color: red; font-weight: bold; text-decoration: none;">worked </ins>in the Firefox web browser. It was designed for students and educators, but because of its power and ease of use, <ins style="color: red; font-weight: bold; text-decoration: none;">was </ins>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.".</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Protein Explorer <del style="color: red; font-weight: bold; text-decoration: none;">utilizes </del>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 <del style="color: red; font-weight: bold; text-decoration: none;">is </del>not open-source, and <del style="color: red; font-weight: bold; text-decoration: none;">has </del>had very little development in <del style="color: red; font-weight: bold; text-decoration: none;">recent years</del>. There <del style="color: red; font-weight: bold; text-decoration: none;">is no </del>Chime <del style="color: red; font-weight: bold; text-decoration: none;">available </del>for Mac OS X, and even on Windows, getting Chime to work <del style="color: red; font-weight: bold; text-decoration: none;">can </del>occasionally <del style="color: red; font-weight: bold; text-decoration: none;">be </del>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, and its development ceased in 2007'''.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Protein Explorer <ins style="color: red; font-weight: bold; text-decoration: none;">utilized </ins>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 <ins style="color: red; font-weight: bold; text-decoration: none;">was </ins>not open-source, and had very little development in <ins style="color: red; font-weight: bold; text-decoration: none;">the early 2000s</ins>. There <ins style="color: red; font-weight: bold; text-decoration: none;">was never a </ins>Chime <ins style="color: red; font-weight: bold; text-decoration: none;"> </ins>for Mac OS X, and even on Windows, getting Chime to work <ins style="color: red; font-weight: bold; text-decoration: none;">was </ins>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 has been declining since about 2005, and its development ceased in 2007'''.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Protein Explorer has been, 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].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Protein Explorer has been, 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].</div></td></tr> </table>

Eric Martz