Ramachandran Plot: Difference between revisions
adding a note: ramachandran does not work for simpilifed model view |
relocating the advice about full model display needed for Ramachandran to work |
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==Other entries in Proteopedia== | |||
Interactive Ramachandran plots can be generated for any entry in Proteopedia with the use of a typed Jmol command<ref>Command defined at [http://chemapps.stolaf.edu/jmol/docs/?search=rama#ramachandran site for official Jmol documentation]</ref>: | Interactive Ramachandran plots can be generated for any entry in Proteopedia with the use of a typed Jmol command<ref>Command defined at [http://chemapps.stolaf.edu/jmol/docs/?search=rama#ramachandran site for official Jmol documentation]</ref>: | ||
#For example, in a new browser window open the entry in Proteopedia for [[1bhl]] | #For example, in a new browser window open the entry in Proteopedia for [[1bhl]] | ||
#If the JSmol panel shows a "Displaying simplified model" message, click on the "load full" orange button below it. Once the model is reloaded, | |||
#Right-click on an empty space of the JSmol panel showing the 3D structure on the page, or click on the JSmol logo (or frank) in the bottom right corner. | #Right-click on an empty space of the JSmol panel showing the 3D structure on the page, or click on the JSmol logo (or frank) in the bottom right corner. | ||
#When the menu comes up, select '''<code>Console</code>''' | #When the menu comes up, select '''<code>Console</code>''' | ||
#Click in the lower text panel of the console that comes up and type the command '''<code>Ramachandran</code>''', followed by the return key. | #Click in the lower text panel 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, or enter into the console <code>model 1.1</code>.) With the console window open, the values will be listed as you click on the spheres. | #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, or enter into the console <code>model 1.1</code>.) With the console window open, the values will be listed as you click on the spheres. | ||
#To limit the plot to displaying certain residues or portions of the structure, you can issue commands in the console, such as <code>display helix</code> or <code>display gly</code>. The latter command will limit the plotted display to just glycine residues. In order to return to showing all values on the plot, issue the command <code>display all</code> in the Jmol console. | #To limit the plot to displaying certain residues or portions of the structure, you can issue commands in the console, such as <code>display helix</code> or <code>display gly</code>. The latter command will limit the plotted display to just glycine residues. In order to return to showing all values on the plot, issue the command <code>display all</code> in the Jmol console. | ||