## Adding Points to the Pharmacophore

This program allows you to explore the effects of adding features to the pharmacophore in your P3D file in a straightforward manner.

### Selecting Atoms

The first step in adding features to the pharmacophore is to select atoms in PyMol that define the feature(s). For single-atom features, such as hydrogen-bond donors, you should select that atom; for multi-atom features, such as aromatic groups, you should select one of the aromatic atoms.

After selecting the atoms, click the `Grab Atoms From PyMol` button at the top of the `Alignment Criteria` page. The new atoms are added at the end of the list of atoms already in the pharmacophore:

By clicking the `Highlight` button next to the feature assignment box for each feature, you can highlight the corresponding atom in the molecular sketch (this is the gray circle in the figure above).

### Assigning Feature Types

To assign a feature type, click the feature assignment box for each new feature and select the appropriate type. The program will only show you feature types that match the atom you selected:

For example, in the illustration above, atom 3 is involved in three different feature types, you must select one for the pharmacophore.

### Defining Distances

After assigning types to the points you added, the last step in updating the pharmacophore is to set the distances between the new feature(s) and the others in the pharmacophore. This is done by clicking the `Grab Distances` button.

When `Grab Distances` is pressed, the software examines reference molecule, calculates the distances between the new features and those already present in the pharmacophore, and adds the new distances to the list of distances at the bottom of the window:

The distance ranges are automatically calculated based on a tolerance value.

Note that the sketch of the pharmacophore on the molecule has also been updated to highlight the atoms in the new feature (drawn with red circles in the sketch).

### Exploring Changes

Once the new pharmacophore has been defined, you can switch back to the `Search Results` tab in order to explore how your current set of molecules can align.

Note: Defining a new pharmacophore will destroy any alignments that you may have found to the current pharmacophore. If you would like to save these, you should Save your work before clicking `Grab Distances`.