I would calculate an omit map. Delete your ligand and use the resulting pdb file to calculate a map. Density for your ligand will show up as positive difference density.

Herman

From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of RONG hui Rong
Sent: Friday, August 26, 2011 4:44 PM
To: [log in to unmask]
Subject: [ccp4bb] Closed density map

Dear all,
Do you know how to generate some closed density map (mesh) that can wrap ligand without tangling with electron density map of other residues?

Many Thanks!

Hui