https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?action=history&feed=atom&title=VMD 2026-05-13T18:36:46Z Revision history for this page on the wiki MediaWiki 1.39.7 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=VMD&diff=2210&oldid=prev 2009-04-02T15:15:29Z

<p><span dir="auto"><span class="autocomment">Tutorials</span></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 15:15, 2 April 2009</td> </tr><tr> <td colspan="2" class="diff-lineno">Line 13:</td> <td colspan="2" class="diff-lineno">Line 13:</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>* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9</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>* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9</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>* making movies from a '.pdb' file containing multiple structures. ''This is dealt with in the OPTIM section as part of the tutorial on making a movie of a path''</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>* making movies from a '.pdb' file containing multiple structures. ''This is dealt with in the OPTIM section as part of the tutorial on making a movie of a path''</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>* [[<del style="font-weight: bold; text-decoration: none;">using</del> <del style="font-weight: bold; text-decoration: none;">Molfacture</del> <del style="font-weight: bold; text-decoration: none;">to</del> <del style="font-weight: bold; text-decoration: none;">edit</del> <del style="font-weight: bold; text-decoration: none;">molecules</del> and <del style="font-weight: bold; text-decoration: none;">add hydrogens</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>* [[<ins style="font-weight: bold; text-decoration: none;">visualising</ins> <ins style="font-weight: bold; text-decoration: none;">normal</ins> <ins style="font-weight: bold; text-decoration: none;">modes</ins> <ins style="font-weight: bold; text-decoration: none;">using</ins> <ins style="font-weight: bold; text-decoration: none;">VMD</ins> and <ins style="font-weight: bold; text-decoration: none;">OPTIM</ins>]]</div></td> </tr> </table>

import>Csw34 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=VMD&diff=2209&oldid=prev 2008-07-25T09:30:35Z

<p>Formatting</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 09:30, 25 July 2008</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-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>It is possible to load most files using command line flags, making loading many frames into different topology files easy. The -f flag indicates that all subsequent files (until the next -f flag or the end) should be loaded into a single molecule. There are also flags for selecting different file types (default is .pdb), most commonly parm7 for topology files generated by Amber and rst7 for restart files generated by Amber. mdcrd files are denoted -crd and periodic mdcrd files -crdbox.</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>It is possible to load most files using command line flags, making loading many frames into different topology files easy. The -f flag indicates that all subsequent files (until the next -f flag or the end) should be loaded into a single molecule. There are also flags for selecting different file types (default is .pdb), most commonly parm7 for topology files generated by Amber and rst7 for restart files generated by Amber. mdcrd files are denoted -crd and periodic mdcrd files -crdbox.</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 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>e.g.</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>e.g. vmd -f first_mol.pdb -f -parm7 second_mol.prmtop -rst7 second_mol.rst -f -parm7 third_mol.prmtop -crdbox third_mol_1st_frame.crd -crdbox third_mol_2nd_frame</div></td> <td colspan="2" class="diff-empty diff-side-added"></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> vmd -f first_mol.pdb \</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> -f -parm7 second_mol.prmtop -rst7 second_mol.rst \</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> -f -parm7 third_mol.prmtop -crdbox third_mol_1st_frames.crd -crdbox third_mol_2nd_frames</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 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>Khs26 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=VMD&diff=2208&oldid=prev 2008-07-25T09:24:18Z

<p>Added command line stuff</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 09:24, 25 July 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"></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>VMD is a molecular visualization program installed on all workstations and clusters. The official documentation can be found [http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html here] with some tutorials [http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html here]. Like gnuplot however, the wealth of options means that often it takes a long time to find the one command you need to use so below you will find some useful basic settings/info for using VMD. For producing graphics for publication, [[Pymol]] is probably a better option as it has a built in ray-tracing routine but for general visualization, VMD is much quicker.</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>VMD is a molecular visualization program installed on all workstations and clusters. The official documentation can be found [http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html here] with some tutorials [http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html here]. Like gnuplot however, the wealth of options means that often it takes a long time to find the one command you need to use so below you will find some useful basic settings/info for using VMD. For producing graphics for publication, [[Pymol]] is probably a better option as it has a built in ray-tracing routine but for general visualization, VMD is much quicker.</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>It is possible to load most files using command line flags, making loading many frames into different topology files easy. The -f flag indicates that all subsequent files (until the next -f flag or the end) should be loaded into a single molecule. There are also flags for selecting different file types (default is .pdb), most commonly parm7 for topology files generated by Amber and rst7 for restart files generated by Amber. mdcrd files are denoted -crd and periodic mdcrd files -crdbox.</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>e.g. vmd -f first_mol.pdb -f -parm7 second_mol.prmtop -rst7 second_mol.rst -f -parm7 third_mol.prmtop -crdbox third_mol_1st_frame.crd -crdbox third_mol_2nd_frame</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>Khs26 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=VMD&diff=2207&oldid=prev 2008-05-12T16:09:22Z

<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 16:09, 12 May 2008</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-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>* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9</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>* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9</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>* making movies from a '.pdb' file containing multiple structures. ''This is dealt with in the OPTIM section as part of the tutorial on making a movie of a path''</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>* making movies from a '.pdb' file containing multiple structures. ''This is dealt with in the OPTIM section as part of the tutorial on making a movie of a path''</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>* [[using Molfacture to edit molecules and add hydrogens]]</div></td> </tr> </table>

import>Csw34 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=VMD&diff=2206&oldid=prev 2008-04-30T18:38:17Z

<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 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>* [[using VMD to display and manipulate '.pdb' files]]</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>* [[using VMD to display and manipulate '.pdb' files]]</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>* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9</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>* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9</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>* making <del style="font-weight: bold; text-decoration: none;">moves</del> from a '.pdb' file containing multiple structures. ''This is dealt with in the OPTIM section as part of the tutorial on making a movie of a path''</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>* making <ins style="font-weight: bold; text-decoration: none;">movies</ins> from a '.pdb' file containing multiple structures. ''This is dealt with in the OPTIM section as part of the tutorial on making a movie of a path''</div></td> </tr> </table>

import>Csw34 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=VMD&diff=2205&oldid=prev 2008-04-29T12:05:18Z

<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 12:05, 29 April 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>* [[using VMD to display and manipulate '.pdb' files]]</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>* [[using VMD to display and manipulate '.pdb' files]]</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>* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9</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>* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9</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>* making moves from a '.pdb' file containing multiple structures. This is dealt with in the OPTIM section as part of the tutorial on making a movie of a path<del style="font-weight: bold; text-decoration: none;">.</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>* making moves from a '.pdb' file containing multiple structures. <ins style="font-weight: bold; text-decoration: none;">''</ins>This is dealt with in the OPTIM section as part of the tutorial on making a movie of a path<ins style="font-weight: bold; text-decoration: none;">''</ins></div></td> </tr> </table>

import>Csw34 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=VMD&diff=2204&oldid=prev 2008-04-29T12:04:55Z

<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>VMD is a molecular visualization program installed on all workstations and clusters. The official documentation can be found [http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html here] with some tutorials [http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html here]. Like gnuplot however, the wealth of options means that often it takes a long time to find the one command you need to use so below you will find some useful basic settings/info for using VMD. For producing graphics for publication, Pymol is probably a better option as it has a built in ray-tracing routine but for general visualization, VMD is much quicker.</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 is a molecular visualization program installed on all workstations and clusters. The official documentation can be found [http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html here] with some tutorials [http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html here]. Like gnuplot however, the wealth of options means that often it takes a long time to find the one command you need to use so below you will find some useful basic settings/info for using VMD. For producing graphics for publication, <ins style="font-weight: bold; text-decoration: none;">[[</ins>Pymol<ins style="font-weight: bold; text-decoration: none;">]]</ins> is probably a better option as it has a built in ray-tracing routine but for general visualization, VMD is much quicker.</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=VMD&diff=2203&oldid=prev 2008-04-29T12:03:31Z

<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, 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>VMD is a molecular visualization program installed on all workstations and clusters. The official documentation can be found [http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html here] with some tutorials [http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html here]. Like gnuplot however, the wealth of options means that often it takes a long time to find the one command you need to use so below you will find some useful basic settings/info for using VMD.</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 is a molecular visualization program installed on all workstations and clusters. The official documentation can be found [http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html here] with some tutorials [http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html here]. Like gnuplot however, the wealth of options means that often it takes a long time to find the one command you need to use so below you will find some useful basic settings/info for using VMD<ins style="font-weight: bold; text-decoration: none;">. For producing graphics for publication, Pymol is probably a better option as it has a built in ray-tracing routine but for general visualization, VMD is much quicker</ins>.</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=VMD&diff=2202&oldid=prev 2008-04-29T12:02:32Z

<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 12:02, 29 April 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>* [[using VMD to display and manipulate '.pdb' files]]</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>* [[using VMD to display and manipulate '.pdb' files]]</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>* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9</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>* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9</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>* making moves from a <del style="font-weight: bold; text-decoration: none;">[</del>.pdb<del style="font-weight: bold; text-decoration: none;">]</del> file containing multiple structures. This is dealt with in the OPTIM section as part of the tutorial on making a movie of a path.</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>* making moves from a <ins style="font-weight: bold; text-decoration: none;">'</ins>.pdb<ins style="font-weight: bold; text-decoration: none;">'</ins> file containing multiple structures. This is dealt with in the OPTIM section as part of the tutorial on making a movie of a path.</div></td> </tr> </table>

import>Csw34 https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=VMD&diff=2201&oldid=prev 2008-04-29T11:47:45Z

<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 11:47, 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 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>VMD is a molecular visualization program installed on all workstations and clusters. The official documentation can be found [http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html here] with some tutorials [http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html here]. Like gnuplot however, the wealth of options means that often it takes a long time to find the one command you need to use so below you will find some useful basic settings/info for using VMD.</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 is a molecular visualization program installed on all workstations and clusters.</div></td> <td colspan="2" class="diff-empty diff-side-added"></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>== Tutorials ==</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>* [[using VMD to display and manipulate '.pdb' files]]</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>* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9</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>* making moves from a [.pdb] file containing multiple structures. This is dealt with in the OPTIM section as part of the tutorial on making a movie of a path.</div></td> </tr> </table>

import>Csw34