How to use "shape feature" in pharmacophore-based screening?

Dear Sir/Madam,

Now I use interaction pharmacophore generation tool to generate 10 pharmacophore models from protein-ligand complex. And I create shape feature based on my input ligand. However, I can't apply this shape feature in pharmacophore screening (Ligand can't map this feature). Please help me to solve this problem, thank you.

Sincerely,

John