## Exploring Hits

When you first expand a mapping, the software will attempt to generate a number of three-dimensional conformations (embeddings in the language of distance geometry) that satisfy the pharmacophore. Depending upon the complexity of the molecule, this may take several seconds. Each of the mapping's embeddings are scored in three different ways:

1. Energy: this is an estimate of the energy of the embedding relative to the energy of the unconstrained molecule. Because this energy is only an estimate, it is possible to see negative energy values; these should not be considered as physically meaningful (i.e. the pharmacophore does not somehow stabilize the molecule).
2. Shape Score: this is a measure of the degree of shape overlap between the embedding and the reference molecule. Higher shape scores indicate better shape matches.
3. Alignment RMS: this is the root-mean-squared distance between the pharmacophore points in the embedding and those in the reference molecule. Lower RMS values indicated better matches.

Further details about the scoring functions can be found in the Scoring Alignments section of the Methodology chapter.

You can change the the sort order of each mapping's embeddings by left clicking the column headings in the results tree.

Left clicking an individual alignment will cause that alignment to be displayed in PyMol. The details of what is displayed are controlled by the view options.

If you would like to see more possible structures for a mapping, right click on the mapping entry in the results tree and select `More Alignments` from the context menu.

Each alignment entry has a checkbox that can be used to flag the alignment for export to an SD file.

Note: In some cases, the software may identify mappings that either cannot be realized by the molecule or that generate structures that are too strained to be chemically reasonable. Expanding these mappings will generate an error message.