Hi Blaine,
I tried using cmd.do() and your suggested command but I'm getting the following
error:
"Warning: failed to fetch from http://files.rcsb.org/download/1%7Cw9.cif.gz
Warning: failed to fetch from
http://ftp.wwpdb.org/pub/pdb/data/structures/divided/mmCIF/%7Cw/1%7Cw9.cif.gz
Warning: failed to fetch from
http://ftp-versioned.wwpdb.org/pdb_versioned/views/latest/coordinates/mmcif/%7Cw/pdb_00001%7Cw9/pdb_00001%7Cw9_xyz.cif.gz
Error-fetch: unable to load '1|w9'."
I also tried just running cmd.do("show cell") but my images still aren't
showing a unit cell.
Many thanks,
Shay
________________________________
From: Mooers, Blaine H.M. (HSC) <[email protected]>
Sent: 30 September 2020 17:14
To: CHAUDHURI, SHAY (PGR) <[email protected]>;
[email protected] <[email protected]>
Subject: RE: Rendering Unit Cell in API
Hi Shay,
cmd.do() allows you to run pml code.
Try
cmd.do("fetch 1lw9;show cell;png testcell.png")
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: CHAUDHURI, SHAY (PGR) [[email protected]]
Sent: Wednesday, September 30, 2020 9:42 AM
To: [email protected]
Subject: [EXTERNAL] [PyMOL] Rendering Unit Cell in API
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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