def animation(self):
from MMTK.Visualization import viewSequence
scale = self.scale_entry.get()
conf = self.mode.universe.configuration()
offset = scale*self.mode
viewSequence(self.mode.universe,
[conf, conf+offset, conf, conf-offset], 1)
def animation(self):
from MMTK.Visualization import viewSequence
scale = self.scale_entry.get()
conf = self.mode.universe.configuration()
offset = scale * self.mode
viewSequence(self.mode.universe,
[conf, conf + offset, conf, conf - offset], 1)
def _animation(self):
first = string.atoi(self.first_step.get())-1
last = string.atoi(self.last_step.get())
skip = string.atoi(self.skip_step.get())
self._makeUniverse()
from MMTK.Visualization import viewSequence
viewSequence(self.universe,
ConfigurationFactory(self.universe, self.inspector,
range(first, last, skip)))
def _animation(self):
first = string.atoi(self.first_step.get()) - 1
last = string.atoi(self.last_step.get())
skip = string.atoi(self.skip_step.get())
self._makeUniverse()
from MMTK.Visualization import viewSequence
viewSequence(
self.universe,
ConfigurationFactory(self.universe, self.inspector,
range(first, last, skip)))
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!
# First, we define the parts of the chain we are interested in.
tip = chain[60:64]
helix = chain[93:101]
# Then we align the two configurations to make the helix match as well
# as possible:
transformation, rms = helix.findTransformation(monomer_configuration)
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!
# First, we define the parts of the chain we are interested in.
tip = chain[60:64]
helix = chain[93:101]
# Then we align the two configurations to make the helix match as well
# as possible:
transformation, rms = helix.findTransformation(monomer_configuration)
