Hi Yeping - 

Looks like the following settings are in play here:

# different cartoon modes
cartoon automatic, alpha1  # for the alpha1 helix
cartoon tube, chain P   # for the orange, green and blue peptides

# hide backbone sticks/lines where cartoon is shown
set cartoon_side_chain_helper, on

# surface transparency
set transparency, 0.5

# to color the surface a different color from the sticks/lines
set surface_color, orange, chain P and resi 5  

Along with showing surface and line representations for the appropriate residues, this should get you pretty close.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jul 10, 2014, at 6:40 AM, sunyeping <sunyeping@aliyun.com> wrote:

Dear all,

Could anyone tell me how the figure attached to the following web site or the attach file is drawn? In What pymol repersentation of the residues is shown?

<figure.tif>------------------------------------------------------------------------------
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