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:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of RONG hui Rong
Sent: Friday, August 26, 2011 4:44 PM
To: CCP4BB@JISCMAIL.AC.UK
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
