Ramachandran Plot: Difference between revisions
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m added general command for making these plots for other Proteopedia entries |
m fixed formatting of commands in how to plot any Proteopedia entry plus minor formatting changes in that section |
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<scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_myoglobin/1'>Ramachandran plot</scene>: Red data points outside of the area expected for α-helix most likely involve residues at the end of the α-helix because often these have angle values that are not typical for α-helix. White points are those for loops and ordered, nonrepetitive structures. The few residues that map to the disallowed region are Gly.<br> | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_myoglobin/1'>Ramachandran plot</scene>: Red data points outside of the area expected for α-helix most likely involve residues at the end of the α-helix because often these have angle values that are not typical for α-helix. White points are those for loops and ordered, nonrepetitive structures. The few residues that map to the disallowed region are Gly.<br> | ||
<scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_myoglobin_model/1'>Return to model</scene> after viewing plot </p> | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_myoglobin_model/1'>Return to model</scene> after viewing plot </p> | ||
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''' | '''CONCANAVALIN A'''<p> | ||
<scene name='User:Karl_Oberholser/Ramachandran_Plots/Concanavalin_a/3'>View of structure</scene>: Twisted β-sheet with small segments of α-helix.<br> | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Concanavalin_a/3'>View of structure</scene>: Twisted β-sheet with small segments of α-helix.<br> | ||
<scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_concanavalin_a/1'>Ramachandran plot</scene>: Most of the yellow points are located in the area for twisted β-sheets where one would expect them, and again the points in the disallowed region are Gly. <br> | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_concanavalin_a/1'>Ramachandran plot</scene>: Most of the yellow points are located in the area for twisted β-sheets where one would expect them, and again the points in the disallowed region are Gly. <br> | ||
<scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_concanavalin_a_model/1'>Return to model</scene> after viewing plot. </p> | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_concanavalin_a_model/1'>Return to model</scene> after viewing plot. </p> | ||
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''' | '''ACETYLCHOLINESTERASE''' <p> | ||
<scene name='User:Karl_Oberholser/Ramachandran_Plots/Acetylcholinesterase/2'>View structure</scene> <br> | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Acetylcholinesterase/2'>View structure</scene> <br> | ||
<scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_acetylcholinesterase/1'>Ramachandran Plot</scene>: Close to equal amounts of α-helix, β-sheet, and ordered, nonrepetitive structures. One important exception to Gly in the disallowed region is Ser:200. Locate this residue that is located in the disallowed region. An interesting aspect concerning Ser:200 is that it is one of a triad of residues that are part of the catalytic site and are involved in the catalytic action of this enzyme. The unique φ and ψ values for Ser:200 is the major factor in positioning the side chain so that it can participate in the catalysis.<br> | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_acetylcholinesterase/1'>Ramachandran Plot</scene>: Close to equal amounts of α-helix, β-sheet, and ordered, nonrepetitive structures. One important exception to Gly in the disallowed region is Ser:200. Locate this residue that is located in the disallowed region. An interesting aspect concerning Ser:200 is that it is one of a triad of residues that are part of the catalytic site and are involved in the catalytic action of this enzyme. The unique φ and ψ values for Ser:200 is the major factor in positioning the side chain so that it can participate in the catalysis.<br> | ||
<scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_ache_model/1'>Return to model</scene> after viewing plot. | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_ache_model/1'>Return to model</scene> after viewing plot.</p> | ||
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''' | '''OTHER ENTRIES IN PROTEOPEDIA''' <p> | ||
Interactive Ramachandran plots can be generated for all entries in Proteopedia with the use of an advanced command. For example, | Interactive Ramachandran plots can be generated for all entries in Proteopedia with the use of an advanced 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. | ||
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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. | |||
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. | |||
