This is a simple script to generate a repeating atom lattice. It just writes atoms in PDB format, and PyMOL will automatically
connect adjacent atoms when loading the PDB file. You may adjust the
c and/or
x_shift,
y_shift arrays to obtain different geometries, and the number of iterations in the loops to adjust the lattice size.
See also the thread on pymol-users mailing list.
<syntaxhighlight lang="python">
from numpy import array
- coordinates of the repeating unit (from cyclohexane)
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])
- template string for PDB hetatom line
s = 'HETATM %4d C03 UNK 1 %8.3f%8.3f%8.3f 0.00 0.00 C '
out = open('lattice.pdb', 'w')
i = 0
for x in range(10):
for y in range(10):
for v in (c + ..→
