Hi,
I have a pharmacophore model created with Common Feature Pharmacophore tool. On the other hand I have ligands used to create pharm. model docked to set of receptors (using external software). What I want to get is to map pharmacophore model on top ranked pairs ligand - receptor. Algoriht my script is following is:

• 
  
• Read pharmacophore model and ligands used to generate hypothesis
  
• Iterate thru ligands and for each read corresponding pair receptor-hit, for each step:
  
• Group newly read molecules (the idea behind it was to tie receptor with ligand so they move together)
  
• Select ligand from pharmacophore and docking output and make tethers
  
• Align molecules
  
• Deselect molecules and proceed to next ligand from pharmacophore model
  
• Save everything as .msv file
  

Everything works fine until alignment step: ligands are not aligned properly, furthermore, tethers are not being reset at the end of alignment process (this may be the source of bad fits) and I couldn't fid the way to delete them on script level. Fitted ligands move separately from receptors they are grouped with.

My questions are
- is it possible to pin pair ligand - receptor together so they act like one molecule?
- is it possible to fit those pairs to pharmacophore model using DSScript?

Thank you in advance for any help
Stefan Mordalski