https://biowerkzeug.org/index.php?action=history&feed=atom&title=Visualization_software 2026-04-21T16:17:48Z Revision history for this page on the wiki MediaWiki 1.45.3 https://biowerkzeug.org/index.php?title=Visualization_software&diff=71&oldid=prev 2008-06-30T19:35:19Z

<p><span class="autocomment">Molecules in 3D</span></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 19:35, 30 June 2008</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l2">Line 2:</td> <td colspan="2" class="diff-lineno">Line 2:</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>== Molecules in 3D ==</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>== Molecules in 3D ==</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>* [[VMD]]; also has extensive analysis and model <del style="font-weight: bold; text-decoration: none;">build </del>capabilities</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>* [[VMD]]; also has extensive analysis and model <ins style="font-weight: bold; text-decoration: none;">building </ins>capabilities</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>* [[pyMol]]</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>* [[pyMol]]</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>* [[chimera]]</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>* [[chimera]]</div></td></tr> </table>

Orbeckst https://biowerkzeug.org/index.php?title=Visualization_software&diff=49&oldid=prev 2008-06-30T15:00:09Z

<p>new; copied from Woolf wiki</p> <p><b>New page</b></p><div>This page collects software that we find useful to display data from running molecular simulations. A special section is dedicated to [[#Rendering|Render]] software that create photorealistic or artistic images from scenes exported from other visualization software.<br /> <br /> == Molecules in 3D ==<br /> * [[VMD]]; also has extensive analysis and model build capabilities<br /> * [[pyMol]]<br /> * [[chimera]]<br /> * [[yasara]]<br /> * [[QuteMol]]<br /> * [[pyQuteMol]]<br /> <br /> == 1D and 2D data ==<br /> * [[xfarbe]], a simple 2D plotter<br /> * [[xmgrace]], for 1D plots and some graph analysis<br /> * gnuplot<br /> * [[matplotlib]], a python based scientific plotting library<br /> * [[R]]<br /> <br /> == 3D data ==<br /> To display 3D data such as densities, you can use a typically insanely powerful 3D visualization package; see for instance this list of [http://prism.dkrz.de/Workpackages/WP4a/Low-End/Packages/WP4a_Low-End_graphic_packages.html graphics packages].<br /> * [http://www.opendx.org/ OpenDX]: list of [http://www.opendx.org/support.html documentation] and [http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm#HDREDF native DX file format]<br /> * viewers based on [http://www.vtk.org/ VTK] such as [http://mayavi.sourceforge.net/ MayaVi]<br /> * [[VMD]] and [[Chimera]]<br /> <br /> == Rendering ==<br /> * [[Raster3D]] (the renderer can be called from [[VMD]]) and VMD&#039;s [[VMD#Tachyon|Tachyon]].<br /> * [[Gelato]]<br /> * [[Pixie]], a Renderman-compatible shader<br /> <br /> [[Category:Visualization]]<br /> [[Category:Software]]</div>

Oliver