[PyMOL] Pymol colors and selections

[Andrew M. G. <gu...@hw...>]

I'm having PYMOL trouble with something that should be easy:

I want to make a green ribbon diagram, a grey transparent surface, and 
then display residue side chains in red underneath.  I'm having trouble 
with selections that set up these three items as discrete things I can 
color as I choose.  The following script changes the ribbon to red 
under red side chain at residue Asp244.  I want the tube to remain 
green and just the side chain be colored red.

Similarly, the surface becomes colored red.  (I was able to solve the 
surface color problem by using a "set surface_color = grey" command but 
I still feel that I'm missing something here.)  I have tried swapping 
the order of the  selections  and colors to no avail...

Thanks for your help.
-Andy


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load PDBs/prot.pdb, prot
cmd.bg_color('white')
util.ray_shadows('light')

set cartoon_fancy_helices=1
cmd.hide("everything","prot)
cmd.hide("lines","prot")
cmd.hide("nonbonded","prot")
set transparency = 0.3

select Cterm=((chain A) and (resi 200:300))
cmd.show("cartoon","Cterm")
cmd.color ("green","Cterm")
cmd.show("surface","Cterm")

select D244 = (chain A & resi 244 & !name N,O,C)
show sticks, D244
cmd.color("red","D244")
----------------------------------------------------------------


--
Andrew M. Gulick, Ph.D.
------------------------------------------------------
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Research Scientist
Hauptman-Woodward Medical Research Institute

Assistant Professor
Dept. of Structural Biology, SUNY at Buffalo

http://www.hwi.buffalo.edu/personnel/Scientist/Gulick/Gulick.html
http://www.buffalo.edu/~amgulick