Hi guys, Thank you so much for the suggestions! The suggestion to "make two objects of your ligand, display one as sphere and the other as stick. Then change the transparency setting for the spheres" works!! This way, the sphere and the stick can colored differently. And, I also found that show the ligand as sphere and change transparency could also show the sphere and stick as the same time, but just in the same color. Thank you so much!
Best, Wei On Mon, Jan 20, 2014 at 6:54 AM, Folmer Fredslund <[email protected]> wrote: > Hi Wei, > > I think it's easier to do with a surface representation. > I'd do something like this: > > #==== start script ==== > fetch 3b6a, async=0 > as cartoon > extract ligand, c. c and organic > util.chainbow("3b6a") > color green, elem c and ligand > color oxygen, elem o and ligand > show surface, ligand > set surface_mode, 1 > set surface_color, yellow > set transparency=.5 > show sticks, ligand > set stick_radius, 0.4 > show sticks, c. c and i. 130 > set cartoon_side_chain_helper, on > zoom ligand > #==== end script ==== > > > > And then you'd have to mess around with the view/colors of course. > > > Hope this helps > Folmer > > ps: there's actually a PyMOL bulletin board :-) > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > 2014/1/20 Wei Shi <[email protected]> > >> Hi all, >> Please see attached Fig where they show the ligand both as sticks and >> spheres at the same time. Does anyone happen to know how to display the >> ligand like this? Thank you so much! >> >> Best, >> Wei >> >> >> > > > -- > Folmer Fredslund >
