Protein Structure Quality Viewer Panel

Analyze the protein in the Workspace and display tabular and graphical reports on its quality, as measured by deviations from reported values.

To open this panel, click the Tasks button and browse to Biologics → Structure Quality Report.
To open this panel from the entry group for the results of a homology modeling or antibody structure prediction job, use the Workflow Action Menu .

  • Features
  • Additional Resources

Protein Structure Quality Viewer Panel Features

Protein table

This table lists the chains in the protein that is analyzed along with various measures of the overall structure quality. You can analyze multiple proteins and they are all listed in the table, and you can select multiple chains in a single protein for reporting, but you cannot select multiple proteins.

Ramachandran Plot tab

This tab displays a Ramachandran plot of the dihedral angles.

Plot toolbar

The toolbar has tools for manipulating the plot and for saving images. The buttons that are common to all plot toolbars are described in the Plot Toolbar topic.

Display area

This area displays the plot, which has the following features:

  • Residue Markers: Glycine is plotted as triangles, proline is plotted as arrows, pre-proline is plotted as squares, isoleucine/valine is plotted as diamonds, and all other residues are plotted as circles.

  • Regions: The plot has three regions, favored, allowed, and disallowed, which are colored by the color scheme selected from the Color option menu.

  • Pausing the cursor over a point displays information for that residue at the top of the panel, and highlights the residue in the Workspace.

  • 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. Click again on the point to deselect it.

Modify appearance of Workspace structure residues in region options

Select options to change the appearance of the residues in the Workspace structure for each of the three regions. The appearance is changed by coloring the residues by the region color and modifying the molecular representation. The coloring is applied when you analyze the Workspace or change the color scheme, so you should set these options first, and then click Analyze Workspace or change the color scheme.

Deselecting any of these options does not revert the color scheme to the original scheme, so you must change the scheme manually to revert it.

Color option menu

Choose the color scheme used in the plot for the favorable, allowed, and disallowed regions. The choices are Green/Cyan/Red and Red/Yellow/White.

Protein Report tab

This tab displays information and a graphical representation of various measures of protein structure quality. You can obtain a PDF report from the command line with the structure_reliability Command Help utility.

Display option menu

Choose the property that you want to display in the table and to plot.

Export and Export All buttons

Export exports the current property table as a text file. Export All exports all property tables as a text file. Both buttons open a file selector in which you can navigate to the location and name the file.

Property table

Displays a list of values of the property chosen from the Display menu. Selecting table rows zooms the Workspace view in to the structural features listed in those rows, highlights them with a change in representation, and selects them. The average of the selected property over the entire structure is displayed below the table.

Property plot area

The property is plotted as a function of the row number in the table in this area. The plot area has a toolbar, which has the same buttons as for the Ramachandran plot. The red dashed horizontal lines and blue dashed vertical lines can be dragged to highlight a portion of the plot of interest, which is given a white background, and the rest is gray. The atoms associated with the highlighted portion of the plot are interactively selected in the Workspace, and the rows for the points in the highlighted region are selected in the table.

Analyze Workspace button

Click the Analyze Workspace button to analyze the protein structure that is displayed in the Workspace, fill in the tables and draw the plots.

Related Topics