Edit Feature X Dialog Box

Edit the properties of a hypothesis feature that is in the Workspace, including position and settings related to screening.

To open this dialog box, right-click on the feature in the Workspace.

  • Using
  • Features
  • Additional Resources

Using the Edit Feature X Dialog Box

To reposition a feature, select Manually reposition feature and then translate or rotate the feature as you normally would for a structure. If you need to change the Workspace camera view to see the feature from a different angle, deselect this option, make the view change, then select it again to make any further adjustments.

Edit Feature X Dialog Box Features

If you open this dialog box while creating a hypothesis from a single ligand, the screening and matching options are not available.

Feature type option

Set the feature type to the type selected from this option menu.

Manually reposition feature option

Reposition the feature by translating or rotating in the Workspace using the mouse. You should use the same actions that you normally use for translating or rotating a structure in the Workspace.

Coordinates text boxes

These text boxes give the x, y, and z coordinates of the feature. The values in these text boxes are updated when you reposition the feature manually. You can also edit the values to reposition the feature.

Usage in screening option menu

Select an option for how the feature is used in screening or hypothesis generation:

  • Disabled—the feature is not available for ligand screening or hypothesis generation, i.e. it is ignored. Once a hypothesis has been generated, any of its permitted or required features can be disabled for screening. This is useful when you want to test the importance of a given feature, for example.

  • Required—the feature must be matched by all hits in ligand screening, and must appear in the final hypothesis in hypothesis generation.

  • Permitted—ligands are permitted to match the feature in ligand screening or hypothesis generation. This is the default.

Allowed to match option menu

Specify the ligand feature types that are permitted to match this feature. The menu is a list of feature types with check boxes that you can use to allow a ligand feature to match the hypothesis feature. The hypothesis feature type is always selected and cannot be deselected.

For example, you might want to allow a hydrophobic feature to also match an aromatic ring. You can allow matches for all features of a given type to another type when doing matching, in the Features tab of the Screening Settings Dialog Box. In this dialog box you can allow matching for specific features. If you allow matches of a vector feature (ring, acceptor, donor) to a non-vector feature (hydrophobic, positive, negative), vector scoring is turned off when you screen ligands for matches to the hypothesis.

Forbidden to match option menu

Specify the ligand feature types that are not permitted to match this feature. The menu is a list of feature types with check boxes that you can use to forbid a ligand feature to match the hypothesis feature. The hypothesis feature type is always unselected and cannot be selected. By default, no ligand features are forbidden to match the hypothesis feature.

This facility is useful when you are using partial matches. After the minimum number of matches has been made, one of the ligand features might be at the same location as one of the unmatched hypothesis features. If this ligand feature isn't the same type as the hypothesis feature that it overlaps, you might want to prevent that from happening. For example, you might want to forbid inadvertent matching of an ionic feature in a ligand to a hydrophobic feature in the hypothesis when the match is not required.

Feature matching tolerance text box

Set the tolerance for matching the feature, in angstroms. If a ligand has a feature of the required type within the specified distance of the hypothesis feature center, the feature is considered to match.

Delete Feature button

Remove the feature from the hypothesis.

Reset button

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

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