https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?action=history&feed=atom&title=Pymol 2026-05-17T23:18:39Z Revision history for this page on the wiki MediaWiki 1.39.7 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=Pymol&diff=2232&oldid=prev 2008-08-16T05:39:48Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 05:39, 16 August 2008</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" data-marker="−"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Pymol is an open-source molecular visualisation program (binaries, full documentation <del style="font-weight: bold; text-decoration: none;">is</del> not freely available, however). Compilation of v1.1 <del style="font-weight: bold; text-decoration: none;">was</del> straightforward (v1.2 is in beta). It is not installed on the clusters. You can find in ''~csw34/bin'' on both clust and mek-quake and run it from there. It is, however, on the SUSE workstations. See the [http://www-theor.ch.cam.ac.uk/IT/software/pymol.html documentation] for details.</div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Pymol is an open-source molecular visualisation program (binaries, full documentation <ins style="font-weight: bold; text-decoration: none;">are</ins> not freely available, however). Compilation of v1.1 <ins style="font-weight: bold; text-decoration: none;">is</ins> straightforward (v1.2 is in beta). It is not installed on the clusters. You can find in ''~csw34/bin'' on both clust and mek-quake and run it from there. It is, however, on the SUSE workstations. See the [http://www-theor.ch.cam.ac.uk/IT/software/pymol.html documentation] for details.</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The advantages Pymol has over [[VMD]] come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment (c) provides a set of libraries that can be called from python. One can run pymol interactively through scripts and not bother with the GUI. It does have downsides, namely that getting many of these options to work is not as easy as with [[VMD]] when you have a simple GUI to work with. It also runs slower as it is more graphics intensive (which is amplified as you're running it over the network) so if you are hoping to visualise a large molecule, [[VMD]] might be a better option. The below tutorials will hopefully illuminate some of the most useful options!</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The advantages Pymol has over [[VMD]] come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment (c) provides a set of libraries that can be called from python. One can run pymol interactively through scripts and not bother with the GUI. It does have downsides, namely that getting many of these options to work is not as easy as with [[VMD]] when you have a simple GUI to work with. It also runs slower as it is more graphics intensive (which is amplified as you're running it over the network) so if you are hoping to visualise a large molecule, [[VMD]] might be a better option. The below tutorials will hopefully illuminate some of the most useful options!</div></td> </tr> </table>

import>Mp466 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=Pymol&diff=2231&oldid=prev 2008-08-15T21:56:12Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 21:56, 15 August 2008</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" data-marker="−"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Pymol is an open-source molecular visualisation program (full documentation is not freely available, however). It is not installed on the clusters. You can find in ''~csw34/bin'' on both clust and mek-quake and run it from there. It is, however, on the SUSE workstations. See the [http://www-theor.ch.cam.ac.uk/IT/software/pymol.html documentation] for details.</div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Pymol is an open-source molecular visualisation program (<ins style="font-weight: bold; text-decoration: none;">binaries, </ins>full documentation is not freely available, however). <ins style="font-weight: bold; text-decoration: none;"> Compilation of v1.1 was straightforward (v1.2 is in beta).</ins> It is not installed on the clusters. You can find in ''~csw34/bin'' on both clust and mek-quake and run it from there. It is, however, on the SUSE workstations. See the [http://www-theor.ch.cam.ac.uk/IT/software/pymol.html documentation] for details.</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> </tr> <tr> <td class="diff-marker" data-marker="−"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The advantages Pymol has over [[VMD]] come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment. It does have downsides, namely that getting many of these options to work is not as easy as with [[VMD]] when you have a simple GUI to work with. It also runs slower as it is more graphics intensive (which is amplified as you're running it over the network) so if you are hoping to visualise a large molecule, [[VMD]] might be a better option. The below tutorials will hopefully illuminate some of the most useful options!</div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The advantages Pymol has over [[VMD]] come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment<ins style="font-weight: bold; text-decoration: none;"> (c) provides a set of libraries that can be called from python. One can run pymol interactively through scripts and not bother with the GUI</ins>. It does have downsides, namely that getting many of these options to work is not as easy as with [[VMD]] when you have a simple GUI to work with. It also runs slower as it is more graphics intensive (which is amplified as you're running it over the network) so if you are hoping to visualise a large molecule, [[VMD]] might be a better option. The below tutorials will hopefully illuminate some of the most useful options!</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Tutorials ==</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Tutorials ==</div></td> </tr> </table>

import>Mp466 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=Pymol&diff=2230&oldid=prev 2008-08-15T21:27:33Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 21:27, 15 August 2008</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" data-marker="−"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Pymol is an open-source molecular visualisation program (full documentation is not freely available, however). It is not installed on<del style="font-weight: bold; text-decoration: none;"> all</del> the clusters<del style="font-weight: bold; text-decoration: none;"> or workstations</del>. You can find in ''~csw34/bin'' on both clust and mek-quake and run it from there. It is, however, on the SUSE workstations. See the [http://www-theor.ch.cam.ac.uk/IT/software/pymol.html documentation] for details.</div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Pymol is an open-source molecular visualisation program (full documentation is not freely available, however). It is not installed on the clusters. You can find in ''~csw34/bin'' on both clust and mek-quake and run it from there. It is, however, on the SUSE workstations. See the [http://www-theor.ch.cam.ac.uk/IT/software/pymol.html documentation] for details.</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The advantages Pymol has over [[VMD]] come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment. It does have downsides, namely that getting many of these options to work is not as easy as with [[VMD]] when you have a simple GUI to work with. It also runs slower as it is more graphics intensive (which is amplified as you're running it over the network) so if you are hoping to visualise a large molecule, [[VMD]] might be a better option. The below tutorials will hopefully illuminate some of the most useful options!</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The advantages Pymol has over [[VMD]] come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment. It does have downsides, namely that getting many of these options to work is not as easy as with [[VMD]] when you have a simple GUI to work with. It also runs slower as it is more graphics intensive (which is amplified as you're running it over the network) so if you are hoping to visualise a large molecule, [[VMD]] might be a better option. The below tutorials will hopefully illuminate some of the most useful options!</div></td> </tr> </table>

import>Csw34 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=Pymol&diff=2229&oldid=prev 2008-08-15T12:03:46Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:03, 15 August 2008</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" data-marker="−"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Pymol is <del style="font-weight: bold; text-decoration: none;">a</del> molecular visualisation program. It is <del style="font-weight: bold; text-decoration: none;">'''NOT'''</del> installed on all the clusters or workstations<del style="font-weight: bold; text-decoration: none;"> as we do not currently have a license</del>. You can find in ''~csw34/bin'' on both clust and mek-quake and run it from there. <del style="font-weight: bold; text-decoration: none;">The</del> <del style="font-weight: bold; text-decoration: none;">advantages</del> <del style="font-weight: bold; text-decoration: none;">Pymol</del> <del style="font-weight: bold; text-decoration: none;">has</del> <del style="font-weight: bold; text-decoration: none;">over [[VMD]] come from (a)</del> the <del style="font-weight: bold; text-decoration: none;">quality</del> <del style="font-weight: bold; text-decoration: none;">of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment</del>. <del style="font-weight: bold; text-decoration: none;">It</del> <del style="font-weight: bold; text-decoration: none;">does</del> <del style="font-weight: bold; text-decoration: none;">have downsides, namely that getting many of these options to work is not as easy as with</del> [<del style="font-weight: bold; text-decoration: none;">[VMD]] when you have a simple GUI to work with</del>. <del style="font-weight: bold; text-decoration: none;">It also runs slower as it is more graphics intensive (which is amplified as you're running it over the network) so if you are hoping to visualise a large molecule, [[VMD]</del>] <del style="font-weight: bold; text-decoration: none;">might</del> <del style="font-weight: bold; text-decoration: none;">be a better option</del>.<del style="font-weight: bold; text-decoration: none;"> The below tutorials will hopefully illuminate some of the most useful options!</del></div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Pymol is <ins style="font-weight: bold; text-decoration: none;">an open-source</ins> molecular visualisation program<ins style="font-weight: bold; text-decoration: none;"> (full documentation is not freely available, however)</ins>.<ins style="font-weight: bold; text-decoration: none;"> </ins> It is <ins style="font-weight: bold; text-decoration: none;">not</ins> installed on all the clusters or workstations. You can find in ''~csw34/bin'' on both clust and mek-quake and run it from there. <ins style="font-weight: bold; text-decoration: none;">It</ins> <ins style="font-weight: bold; text-decoration: none;">is,</ins> <ins style="font-weight: bold; text-decoration: none;">however,</ins> <ins style="font-weight: bold; text-decoration: none;">on</ins> the <ins style="font-weight: bold; text-decoration: none;">SUSE</ins> <ins style="font-weight: bold; text-decoration: none;">workstations</ins>. <ins style="font-weight: bold; text-decoration: none;">See</ins> <ins style="font-weight: bold; text-decoration: none;">the</ins> [<ins style="font-weight: bold; text-decoration: none;">http://www-theor.ch</ins>.<ins style="font-weight: bold; text-decoration: none;">cam.ac.uk/IT/software/pymol.html</ins> <ins style="font-weight: bold; text-decoration: none;">documentation</ins>] <ins style="font-weight: bold; text-decoration: none;">for</ins> <ins style="font-weight: bold; text-decoration: none;">details</ins>.</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><br /></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The advantages Pymol has over [[VMD]] come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment. It does have downsides, namely that getting many of these options to work is not as easy as with [[VMD]] when you have a simple GUI to work with. It also runs slower as it is more graphics intensive (which is amplified as you're running it over the network) so if you are hoping to visualise a large molecule, [[VMD]] might be a better option. The below tutorials will hopefully illuminate some of the most useful options!</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Tutorials ==</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Tutorials ==</div></td> </tr> <tr> <td colspan="2" class="diff-lineno">Line 7:</td> <td colspan="2" class="diff-lineno">Line 9:</td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[saving your current setup for future review]]</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[saving your current setup for future review]]</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[advanced colouring]]</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[advanced colouring]]</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><br /></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>== Links == </div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><br /></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [http://pymol.sourceforge.net/ Pymol homepage]</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [http://www.pymolwiki.org/index.php/Main_Page Community wiki]</div></td> </tr> </table>

import>Jss43 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=Pymol&diff=2228&oldid=prev 2008-08-15T11:53:51Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 11:53, 15 August 2008</td> </tr><tr> <td colspan="2" class="diff-lineno">Line 6:</td> <td colspan="2" class="diff-lineno">Line 6:</td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[producing sexy ray-traced images]]</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[producing sexy ray-traced images]]</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[saving your current setup for future review]]</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[saving your current setup for future review]]</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [[advanced colouring]]</div></td> </tr> </table>

import>Khs26 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=Pymol&diff=2227&oldid=prev 2008-06-16T12:56:30Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:56, 16 June 2008</td> </tr><tr> <td colspan="2" class="diff-lineno">Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[changing the representation of your molecule (lines, sticks, cartoon, ribbon etc)]]</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[changing the representation of your molecule (lines, sticks, cartoon, ribbon etc)]]</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[handling multiple structures - alignment, display and orientation]]</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[handling multiple structures - alignment, display and orientation]]</div></td> </tr> <tr> <td class="diff-marker" data-marker="−"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* [[producing ray-traced images]]</div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [[producing<ins style="font-weight: bold; text-decoration: none;"> sexy</ins> ray-traced images]]</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[saving your current setup for future review]]</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[saving your current setup for future review]]</div></td> </tr> </table>

import>Csw34 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=Pymol&diff=2226&oldid=prev 2008-04-30T18:39:50Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:39, 30 April 2008</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" data-marker="−"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Pymol is a molecular visualisation program. It is '''NOT''' installed on all the clusters or workstations as we do not currently have a license. You can find in ''~csw34/bin'' on both clust and mek-quake and run it from there. The advantages Pymol has over [[VMD]] come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment. It does have downsides, namely that getting many of these options to work is not as easy as with [[VMD]] when you have a GUI to work with. It also runs slower as it is more graphics intensive so if you are hoping to visualise a large molecule, [[VMD]] might be a better option. The below tutorials will hopefully illuminate some of the most useful options!</div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Pymol is a molecular visualisation program. It is '''NOT''' installed on all the clusters or workstations as we do not currently have a license. You can find in ''~csw34/bin'' on both clust and mek-quake and run it from there. The advantages Pymol has over [[VMD]] come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment. It does have downsides, namely that getting many of these options to work is not as easy as with [[VMD]] when you have a<ins style="font-weight: bold; text-decoration: none;"> simple</ins> GUI to work with. It also runs slower as it is more graphics intensive<ins style="font-weight: bold; text-decoration: none;"> (which is amplified as you're running it over the network)</ins> so if you are hoping to visualise a large molecule, [[VMD]] might be a better option. The below tutorials will hopefully illuminate some of the most useful options!</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Tutorials ==</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Tutorials ==</div></td> </tr> </table>

import>Csw34 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=Pymol&diff=2225&oldid=prev 2008-04-30T18:38:54Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:38, 30 April 2008</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" data-marker="−"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Pymol is a molecular visualisation program. It is '''NOT''' installed on all the clusters or workstations as we do not have a license. You can find in ''~csw34/bin'' on both clust and mek-quake and run it from there. The advantages Pymol has over [[VMD]] come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment. It does have downsides, namely that getting many of these options to work is not as easy as with [[VMD]] when you have a GUI to work with. It also runs slower as it is more graphics intensive so if you are hoping to visualise a large molecule, [[VMD]] might be a better option. The below tutorials will hopefully illuminate some of the most useful options!</div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Pymol is a molecular visualisation program. It is '''NOT''' installed on all the clusters or workstations as we do not<ins style="font-weight: bold; text-decoration: none;"> currently</ins> have a license. You can find in ''~csw34/bin'' on both clust and mek-quake and run it from there. The advantages Pymol has over [[VMD]] come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment. It does have downsides, namely that getting many of these options to work is not as easy as with [[VMD]] when you have a GUI to work with. It also runs slower as it is more graphics intensive so if you are hoping to visualise a large molecule, [[VMD]] might be a better option. The below tutorials will hopefully illuminate some of the most useful options!</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Tutorials ==</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Tutorials ==</div></td> </tr> </table>

import>Csw34 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=Pymol&diff=2224&oldid=prev 2008-04-29T12:04:36Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:04, 29 April 2008</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" data-marker="−"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Pymol is a molecular visualisation program. It is '''NOT''' installed on all the clusters or workstations as we do not have a license. You can find in ''~csw34/bin'' on both clust and mek-quake and run it from there. The advantages Pymol has over VMD come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment. It does have downsides, namely that getting many of these options to work is not as easy as with VMD when you have a GUI to work with. The below tutorials will hopefully illuminate some of the most useful options!</div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Pymol is a molecular visualisation program. It is '''NOT''' installed on all the clusters or workstations as we do not have a license. You can find in ''~csw34/bin'' on both clust and mek-quake and run it from there. The advantages Pymol has over <ins style="font-weight: bold; text-decoration: none;">[[</ins>VMD<ins style="font-weight: bold; text-decoration: none;">]]</ins> come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment. It does have downsides, namely that getting many of these options to work is not as easy as with <ins style="font-weight: bold; text-decoration: none;">[[</ins>VMD<ins style="font-weight: bold; text-decoration: none;">]]</ins> when you have a GUI to work with<ins style="font-weight: bold; text-decoration: none;">. It also runs slower as it is more graphics intensive so if you are hoping to visualise a large molecule, [[VMD]] might be a better option</ins>. The below tutorials will hopefully illuminate some of the most useful options!</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Tutorials ==</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Tutorials ==</div></td> </tr> </table>

import>Csw34 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=Pymol&diff=2223&oldid=prev 2008-04-29T11:58:22Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 11:58, 29 April 2008</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" data-marker="−"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Pymol is a molecular visualisation program. It is NOT installed on all the clusters or workstations as we do not have a license. You can find in ~csw34/bin on both clust and mek-quake and run it from there. The advantages Pymol has over VMD come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment. It does have downsides, namely that getting many of these options to work is not as easy as with VMD when you have a GUI to work with. The below tutorials will hopefully illuminate some of the most useful options!</div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Pymol is a molecular visualisation program. It is <ins style="font-weight: bold; text-decoration: none;">'''</ins>NOT<ins style="font-weight: bold; text-decoration: none;">'''</ins> installed on all the clusters or workstations as we do not have a license. You can find in <ins style="font-weight: bold; text-decoration: none;">''</ins>~csw34/bin<ins style="font-weight: bold; text-decoration: none;">''</ins> on both clust and mek-quake and run it from there. The advantages Pymol has over VMD come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment. It does have downsides, namely that getting many of these options to work is not as easy as with VMD when you have a GUI to work with. The below tutorials will hopefully illuminate some of the most useful options!</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Tutorials ==</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Tutorials ==</div></td> </tr> </table>

import>Csw34