RE: [PyMOL] Pymol colors and selections

[Warren D. <wa...@de...>]

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           
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. mailto:wa...@de...      
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Andrew M.Gulick
> Sent: Monday, May 23, 2005 9:00 AM
> To: pym...@li...; cc...@dl...
> 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
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> ------------------------------------------------------
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> 
> Assistant Professor
> Dept. of Structural Biology, SUNY at Buffalo
> 
> http://www.hwi.buffalo.edu/personnel/Scientist/Gulick/Gulick.html
> http://www.buffalo.edu/~amgulick
> 
>