Hi Yangming, If you change the HETATM records of the ligand to ATOM records in the PDB file, you can replace the spheres for a surface representation, for which you can set the transparancy to make it less visible, that might help.
Flip -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Yanming Zhang Sent: Monday, October 29, 2007 6:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] pymol help Hi, all, I want to make a pymol figure wich can show the pretty density of a ligand. But we don't want to show the detailed chemical info of the ligand. If I use a large enough sphere_scale for the ligand, the chemical info will be hidden but the density map will be disrupted. If I use a smaller sphere_scale, the density looks great but the chemical info of the ligand will be visible. How should I overcome this dilemma? Thank you very much for your help. Yanming
