Ramachandran Plot: Difference between revisions

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'''OTHER ENTRIES IN PROTEOPEDIA''' <p>

Interactive Ramachandran plots can be generated for any entry in Proteopedia with the use of an advanced [http://chemapps.stolaf.edu/jmol/docs/?search=rama#ramachandran Jmol] command. For example, in a new browser window open the entry in Proteopedia for [[1bhl]] and in the Jmol scene window that comes up on the right, click on the Jmol frank in the bottom right corner. When the menu comes up, select '''<code>Console</code>''' and then click in the lower text window of the console that comes up and type the command '''<code>Ramachandran</code>''' , followed by the return key. After some processing the Ramachandran plot will be visible and you can hover over and click on the points in the plot just as you can with atoms in a Jmol scene window.

Interactive Ramachandran plots can be generated for any entry in Proteopedia with the use of an advanced [http://chemapps.stolaf.edu/jmol/docs/?search=rama#ramachandran Jmol] command. For example, in a new browser window open the entry in Proteopedia for [[1bhl]] and in the Jmol scene window that comes up on the right, click on the Jmol frank in the bottom right corner. When the menu comes up, select '''<code>Console</code>''' and then click in the lower text window of the console that comes up and type the command '''<code>Ramachandran</code>''' , followed by the return key. After some processing the Ramachandran plot will be visible and you can hover over and click on the points in the plot just as you can with atoms in a Jmol scene window. To return to the model, an easy solution is to reload the page or open a new browser instance of that page.

<br>

This method to generate interactive Ramachandran plots will also work for other instances of the Jmol applet elsewhere on the web if the version of the Jmol is 11.4 or greater.<br>

If you just need to report φ and ψ values for a few residues, use the Scene Authoring Tools to select the residues of interest and enter the command '''<code> draw RAMACHANDRAN </code>''' in the console.

Ramachandran Plot: Difference between revisions

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 '''OTHER ENTRIES IN PROTEOPEDIA''' <p>
-Interactive Ramachandran plots can be generated for any entry in Proteopedia with the use of an advanced [http://chemapps.stolaf.edu/jmol/docs/?search=rama#ramachandran Jmol] command. For example, in a new browser window open the entry in Proteopedia for [[1bhl]] and in the Jmol scene window that comes up on the right, click on the Jmol frank in the bottom right corner. When the menu comes up, select '''<code>Console</code>''' and then click in the lower text window of the console that comes up and type the command  '''<code>Ramachandran</code>''' , followed by the return key. After some processing the Ramachandran plot will be visible and you can hover over and click on the points in the plot just as you can with atoms in a Jmol scene window.
+Interactive Ramachandran plots can be generated for any entry in Proteopedia with the use of an advanced [http://chemapps.stolaf.edu/jmol/docs/?search=rama#ramachandran Jmol] command. For example, in a new browser window open the entry in Proteopedia for [[1bhl]] and in the Jmol scene window that comes up on the right, click on the Jmol frank in the bottom right corner. When the menu comes up, select '''<code>Console</code>''' and then click in the lower text window of the console that comes up and type the command  '''<code>Ramachandran</code>''' , followed by the return key. After some processing the Ramachandran plot will be visible and you can hover over and click on the points in the plot just as you can with atoms in a Jmol scene window. To return to the model, an easy solution is to reload the page or open a new browser instance of that page.
 <br>
 This method to generate interactive Ramachandran plots will also work for other instances of the Jmol applet elsewhere on the web if the version of the Jmol is 11.4 or greater.<br>
 If you just need to report &phi; and &psi; values for a few residues, use the Scene Authoring Tools to select the residues of interest and enter the command  '''<code> draw RAMACHANDRAN </code>'''  in the console.