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# This example shows how to construct the unit cell and images of the
# unit cell from the information in a PDB file.
#
# Note that this will not necessarily work with any PDB file. Many files
# use non-crystallographic symmetry information in a non-standard way.
# This is usually explained in REMARK records, but those cannot be
# evaluated automatically.
#
from MMTK import *
from MMTK.PDB import PDBConfiguration
# A utility function that creates an image of an object by making
# a copy and applying a transformation to the copy.
def makeImage(object, transformation):
image = deepcopy(object)
for atom in image.atomList():
atom.setPosition(transformation(atom.position()))
return image
# Read PDB configuration and create MMTK objects for all peptide chains.
# A C-alpha model is used to reduce the system size. You can remove
# 'model="calpha"' to get an all-atom model, but for insulin this will
# create more than 380000 atoms for the 27-unit-cell crystal!
conf = PDBConfiguration('insulin.pdb')
chains = Collection(conf.createPeptideChains(model="calpha"))
# Apply non-crystallographic symmetries to construct the asymmetric unit
asu = Collection(chains)
for so in conf.ncs_transformations:
if not so.given:
image = makeImage(chains, so)
asu.addObject(image)
# Apply crystallographic symmetries to construct the unit cell
# Note that the list of crystallographic symmetries includes the
# identity transformation, so the unmodified asu is not added
# to the unit cell.
cell = Collection()
for so in conf.cs_transformations:
image = makeImage(asu, so)
cell.addObject(image)
# Translate the image such that its center of mass is
# located inside the unit cell.
cm = image.centerOfMass()
cm_fract = conf.to_fractional(cm)
cm_fract = Vector(cm_fract[0] % 1., cm_fract[1] % 1., cm_fract[2] % 1.)
cm = conf.from_fractional(cm_fract)
image.translateTo(cm)
# Write the unit cell to a PDB file
cell.writeToFile('insulin_unit_cell.pdb')
# Construct the base vectors of the unit cell
e1 = conf.from_fractional(Vector(1., 0., 0.))
e2 = conf.from_fractional(Vector(0., 1., 0.))
e3 = conf.from_fractional(Vector(0., 0., 1.))
# Add the 26 nearest neighbour images of the unit cell
universe = InfiniteUniverse()
for i in [-1, 0, 1]:
for j in [-1, 0, 1]:
for k in [-1, 0, 1]:
image = deepcopy(cell)
image.translateBy(i*e1+j*e2+k*e3)
universe.addObject(image)
# Write the crystal to a PDB file
universe.writeToFile('insulin_crystal.pdb')
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