Pyadmin: 1 revision

2014-03-28T01:47:13Z

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Speleo3: created

2013-01-04T17:18:50Z

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This is a simple script to generate a repeating atom lattice. It just writes atoms in PDB format, and PyMOL will automatically [[connect_mode|connect adjacent atoms]] when loading the PDB file. You may adjust the <code>c</code> and/or <code>x_shift</code>, <code>y_shift</code> arrays to obtain different geometries, and the number of iterations in the loops to adjust the lattice size.

See also the [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11139.html 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 + (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'
</syntaxhighlight>

[[Category:Script_Library]]

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