def view(self, scale=1., color=None):
"""Shows a graphical representation of the field using
a VRML viewer. All values are multiplied by |scale|. |color|
permits the choice of a color for the graphics objects."""
from Scientific.Visualization import VRML
objects = self.graphicsObjects(scale=scale,
color=color,
graphics_module=VRML)
VRML.Scene(objects).view()
def writeToFile(self, filename, scale=1., color=None):
"""Writes a graphical representation of the field
to the VRML file named by |filename|, multiplying
all values by |scale|. |color| permits the choice
of a color for the graphics objects."""
from Scientific.Visualization import VRML
objects = self.graphicsObjects(scale=scale,
color=color,
graphics_module=VRML)
VRML.Scene(objects).writeToFile(filename)
chain.applyTransformation(transformation)
# Let's calculate the local deformation due to the change in conformation
# for each atom. Small values indicate rigid regions and large values
# indicate flexible regions. The visualization requires a VRML viewer.
# Reference: K. Hinsen, A. Thomas, M.J. Field: Proteins 34, 369 (1999)
from MMTK.Deformation import FiniteDeformationFunction
from Scientific.Visualization import VRML
difference = monomer_configuration - universe.configuration()
deformation_function = FiniteDeformationFunction(universe, 0.3, 0.6)
deformation = deformation_function(difference)
graphics = universe.graphicsObjects(color_values=deformation,
graphics_module=VRML)
VRML.Scene(graphics).view()
# The deformation shows a small rigid region and a much larger
# more flexible region.
# Action: We show an animation of the two configurations. This requires
# an animation-capable external viewer, e.g. VMD.
from MMTK.Visualization import viewSequence
viewSequence(chain, [universe.configuration(), monomer_configuration])
# Interesting: there's a floppy loop with residues Gln61, Glu62, and Glu63
# at the tip. It seems to do a funny rotation relative to a closeby helix
# (His94-Lys101) when switching between the two configurations. Let's
# find out what this rotation is!