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As an example for using PyMOL, we will render a cartoon image of a protein (1bl8). If you would like to repeat the example, then please start an interactive PyMOL session on a login node and type the following sequence of commands in PyMOL

fetch 1bl8
show cartoon
hide lines, all
set depth_cue, 0
set spec_reflect, 0
set bg_rgb=[1,1,1]
set orthoscopic, on
set cartoon_fancy_helices, 1
set cartoon_smooth_loops, 1
set cartoon_highlight_color, 1
set ray_shadows, 0
set ray_texture, 1

This is, what the result should then look like:

PyMOL example for rendering a protein. Please click on the picture to see a larger version