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
