Andrew,
Here's how I would write that script:
load PDBs/prot.pdb, prot
bg_color white
util.ray_shadows('light')
set cartoon_fancy_helices, 1
hide everything, prot
select Cterm, A/200-300/
show cartoon, Cterm
set cartoon_color, green
show surface, Cterm
set transparency, 0.3
set surface_color, grey
select D244, A/244/
color red, D244
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:[email protected]
> -----Original Message-----
> From: [email protected]
> [mailto:[email protected]] On Behalf Of
> Andrew M.Gulick
> Sent: Monday, May 23, 2005 9:00 AM
> To: [email protected]; [email protected]
> Subject: [PyMOL] Pymol colors and selections
>
> 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
>
>
> -------------------------------------------------------
> 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.
> ------------------------------------------------------
> NEW CONTACT INFO 4/1/2005
> (716) 898-8619
> Hauptman-Woodward Institute
> 700 Ellicott St Buffalo, NY 14203
> ------------------------------------------------------
> 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
>
>
