Hi Shay,
I think the unit cell is simply clipped off with how you set up the camera
view. Try calling "clip" after every "zoom" call, like this:
cmd.zoom(complete=1)
cmd.clip("slab", 100)
Cheers,
Thomas
> On Sep 30, 2020, at 4:42 PM, CHAUDHURI, SHAY (PGR)
> <s.chaudh...@warwick.ac.uk> wrote:
>
> 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
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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