Ramachandran Plot Panel |
This panel displays a Ramachandran plot of the protein dihedrals φ and ψ.
To open the Ramachandran Plot panel, you can:
Choose Tools → Ramachandran Plot in the main window.
Choose Tasks → Protein Analysis → Ramachandran Plot in the main window.
Click Protein Reports in the Protein Preparation Wizard panel
This panel is useful for identifying residues that fall in disallowed regions of protein dihedrals, so that adjustments can be made to the protein geometry. Once you have adjusted the geometry, click Refresh to redisplay the plot. You can only display a plot for one entry at a time.
The toolbar provides tools for manipulation of the plot and for saving an image of the plot. This is a generic toolbar, and some of the actions may not be useful or relevant. The toolbar buttons are described below.
Reset Reset the plot to the original pan and zoom settings. |
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Back Display the previous view of the plot in the view history. |
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Forward Display the next view of the plot in the view history. |
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Pan/zoom Pan the plot by dragging with the left mouse button, zoom by dragging with the right button. |
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Zoom to rectangle Drag out a rectangle on the plot to zoom in to that rectangle. |
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Configure subplots Configure the margins and spacing of each plot in the panel. |
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Save image Save an image of the plot to file. Opens a file selector in which you can browse to a location, select the image format, and name the image. |
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Edit axis and curve parameters Make settings for the title, range, labeling, and scale of the axes; the color, style, and width of lines; and the color, style, and size of markers. |
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Copy image Copy an image of the plot to the clipboard, so you can paste it into another application. This button is only available in some panels. |
The plot area displays a plot of protein dihedrals for all residues in the protein. The plot has the following features:
Glycine is plotted as triangles, proline is plotted as squares, all other residues are plotted as circles.
The orange regions are the "favored" regions, the yellow regions are the "allowed" regions, and the white regions are the "disallowed" regions.
Pausing the pointer over a point displays information for that residue at the top of the panel, and highlights the residue in the Workspace sequence viewer. If another point is selected, the information for the selected point is replaced while the pointer is over the current point, and returns when the pointer moves off the current point.
Clicking on a point selects the point, zooms the Workspace image in to that residue, and highlights it with pale yellow markers. The point is displayed as an outline instead of solid black. The residue information is displayed at the top of the panel.
Reanalyze the protein and redisplay the plot.
Use this slider to adjust the size of the points in the plot.
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