Hi James,
just calculate the coordinates and write them out in PDB format, quite
simple task. Try the attached script.
Cheers,
Thomas
James Starlight wrote, On 01/04/13 09:14:
> Hi Mike,
>
> Chimera can build such lattices by means of it's build structure
> module. On other hand I want to build such 2D lattices
> http://imageshack.us/photo/my-images/543/lattice.png/
> made from SP3 carbons as the nodes via some automatic script to
> obtain lattices with desired dimensions.
>
> James
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
from numpy import array
s = 'HETATM %4d C03 UNK 1 %8.3f%8.3f%8.3f 0.00 0.00 C '
c = array([[ 0.064, 2.851, -1.085 ],
[ 0.260, 1.969, 0.159 ]])
x_shift = array([ 1.67441517, -0.91605961, 1.66504574])
y_shift = array([-0.69477826, -0.40578592, 2.40198410])
out = open('lattice.pdb', 'w')
i = 0
for x in range(10):
for y in range(10):
for v in (c + (x-y/2) * x_shift + y * y_shift):
i += 1
print >> out, s % (i, v[0], v[1], v[2])
out.close()
try:
from pymol import cmd
cmd.load('lattice.pdb')
except ImportError:
print 'Please load lattice.pdb with PyMOL'
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