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No surface?
If you find unwanted holes in your surface or not all atoms are shown as surface (e.g. ligands), it might be due to the ignore flag or to the surface_mode. Maybe this helps:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05586.html
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00136.html
With my examples, only the flag helped and I didn't really understand what's going on. Maybe somebody else wants to put this in the page. --Karo 12:23, 31 August 2010 (UTC)