Protein Surface Analyzer - Settings Dialog Box

Make settings for the display of the protein surface analysis and for the inclusion of heterogroups in the analysis.

To open this dialog box, click the Settings button in the Protein Surface Analyzer Panel.

  • Features
  • Additional Resources

Protein Surface Analyzer - Settings Dialog Box Features

Patch size and color settings

These controls allow you to change the size and color of the patches on the surface. The same set of controls is available for each patch type (positive, negative, and hydrophobic).

Size Cutoff text boxes

Enter the minimum surface area in Å2 for a patch of the given type to be displayed. Patches with a smaller surface area are not colored with the color for the patch type, but have the default color.

Value Cutoff text boxes

Enter the cutoff for the potential or the SlogP value for points on the surface to be included in a patch. A larger (absolute) value results in smaller patches with a larger strength value.

Color option menus

Select the color for the surface patches, from a set of distinct colors.

Transparency controls

These controls affect how transparent or opaque the surface is.

Front surface and Back surface sliders

Drag the slider to change the transparency of the front or back of the surface, or enter the transparency in the text box.

Adjust together option

Select this option (the default) to apply the same transparency to both front and back of the surface. When selected, dragging one slider or entering a value in one of the text boxes changes the value for the other side of the surface. Deselect this option to adjust the transparency of the front and back of the surface independently.

Include heterogroups section

Specify the hetero groups that are to be included in the surface generation and analysis. By default, ligands that are covalently bound to the protein are included in the surface.

If no groups appear in the list, you may need to change the settings for detecting ligands. Click the Ligand Detection Settings button, and change the settings, then close and reopen this dialog box to see the changes.

Search text box

Filter the list of groups by their identifier in the list (chain, residue number, 3-letter code). To return to the full list, clear the text box.

Heterogroup list

List of hetero groups that are available for inclusion in the surface calculation and patch analysis, i.e. can be considered part of the protein for the purpose of analyzing its surface. The hetero groups are identified by their chain name, residue number, and 3-letter residue code, e.g. A:153 (HEM). The check box to the left of each group allows you to include it in or exclude it from the analysis.

Include buttons

These buttons allow you to select various sets of hetero groups for inclusion in the analysis.

  • All—include all hetero groups in the analysis.
  • Invert—switch the included and excluded hetero groups (include the excluded groups and exclude the included groups). This is useful if you want to exclude a few groups for example: select the groups to exclude in the list, click Selected, then click Invert.
  • Shown—include in the analysis the hetero groups that are shown in the list. This can be used with the search filter to reduce the
  • Selected—include in the analysis the hetero groups that are selected in the list.
Ligand Detection Settings button

Open the Preferences panel with the Ligand Detection Preferences settings displayed. Changing these settings changes what is shown in the list of hetero groups. Note that these settings are global, and will affect detection of ligands in all Maestro panels, not just the Protein Surface Analyzer panel. You might want to revert the settings after doing the analysis.

Restore Defaults button

Restore all settings in the dialog box to their default values.

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