[PyMOL] Rendering Unit Cell in API

[CHAUDHURI, S. (PGR) <S.C...@wa...>]

Hi all,

I'm trying to generate a series of rendered images using the API. The script itself works fine but the only thing that isn't being rendered is the unit cell. I have been using the cmd.show(representation='cell') command to try and get the unit cell to show but it doesn't appear to be working and there is no documentation on how to show the unit cell using the API.

This is one of the structures I have been trying to render (called "structure.pdb"):
CRYST1 2.526 3.572 40.104 90.00 90.00 90.00 P 1
MODEL 1
ATOM 0 C MOL 1 -0.018 2.808 5.068 1.00 0.00 C
ATOM 1 C MOL 1 1.245 1.012 6.314 1.00 0.00 C
ATOM 2 C MOL 1 1.245 1.920 5.067 1.00 0.00 C
ATOM 3 C MOL 1 -0.018 0.143 6.315 1.00 0.00 C
ATOM 4 C MOL 1 -0.017 2.833 7.563 1.00 0.00 C
ATOM 5 C MOL 1 1.245 1.895 7.564 1.00 0.00 C
ATOM 6 O MOL 1 -0.017 -0.218 8.794 1.00 0.00 O
ATOM 7 O MOL 1 1.245 1.373 8.794 1.00 0.00 O
ATOM 8 C MOL 1 -0.018 6.380 5.068 1.00 0.00 C
ATOM 9 C MOL 1 1.245 4.584 6.314 1.00 0.00 C
ATOM 10 C MOL 1 1.245 5.492 5.067 1.00 0.00 C
ATOM 11 C MOL 1 -0.018 3.715 6.315 1.00 0.00 C
ATOM 12 C MOL 1 -0.017 6.405 7.563 1.00 0.00 C
ATOM 13 C MOL 1 1.245 5.467 7.564 1.00 0.00 C
ATOM 14 O MOL 1 -0.017 3.354 8.794 1.00 0.00 O
ATOM 15 O MOL 1 1.245 4.945 8.794 1.00 0.00 O
ATOM 16 C MOL 1 2.508 2.808 5.068 1.00 0.00 C
ATOM 17 C MOL 1 3.771 1.012 6.314 1.00 0.00 C
ATOM 18 C MOL 1 3.771 1.920 5.067 1.00 0.00 C
ATOM 19 C MOL 1 2.508 0.143 6.315 1.00 0.00 C
ATOM 20 C MOL 1 2.509 2.833 7.563 1.00 0.00 C
ATOM 21 C MOL 1 3.771 1.895 7.564 1.00 0.00 C
ATOM 22 O MOL 1 2.509 -0.218 8.794 1.00 0.00 O
ATOM 23 O MOL 1 3.771 1.373 8.794 1.00 0.00 O
ATOM 24 C MOL 1 2.508 6.380 5.068 1.00 0.00 C
ATOM 25 C MOL 1 3.771 4.584 6.314 1.00 0.00 C
ATOM 26 C MOL 1 3.771 5.492 5.067 1.00 0.00 C
ATOM 27 C MOL 1 2.508 3.715 6.315 1.00 0.00 C
ATOM 28 C MOL 1 2.509 6.405 7.563 1.00 0.00 C
ATOM 29 C MOL 1 3.771 5.467 7.564 1.00 0.00 C
ATOM 30 O MOL 1 2.509 3.354 8.794 1.00 0.00 O
ATOM 31 O MOL 1 3.771 4.945 8.794 1.00 0.00 O
ENDMDL

This is my rendering script:


from pymol import cmd

#Viewing settings
cmd.load("structure.pdb")
cmd.set('orthoscopic', 1)
cmd.show(representation='cell')

#Ball-and-stick model
cmd.show('spheres')
cmd.set('sphere_scale', 0.33)
cmd.show('sticks')
cmd.set('stick_radius', 0.2)

#Colours
cmd.color('grey', 'name C*')
cmd.set('stick_transparency', 0.05)
cmd.bg_color('white')
cmd.set('ray_opaque_background', 0)
cmd.set('ray_shadow', 0)

#Render image
basename = 'Structure'
cmd.zoom(complete=1)
cmd.ray(1024, 1024)
cmd.png(basename+'_Z'+'.png', dpi=600)

cmd.rotate('y',-90)
cmd.rotate('z',-90)
cmd.ray(1024, 1024)
cmd.zoom(complete=1)
cmd.png(basename+'_X'+'.png', dpi=600)

cmd.rotate('z',-90)
cmd.rotate('x',-90)
cmd.rotate('z', 90)
cmd.ray(1024)
cmd.zoom(complete=1)
cmd.png(basename+'_Y'+'.png', dpi=600)

cmd.quit()


Many thanks,


Shay Chaudhuri