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.


Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center

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?

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