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# Example: Vector field visualization of the slowest normal mode of insulin.
#
# This example shows the use of vector fields in the analysis and
# visualization of collective motions. For a more elaborate application,
# see
# A. Thomas, K. Hinsen, M.J. Field, D. Perahia
# Tertiary and quaternary confrmational changes in aspartate
# transcarbamylase: a normal mode study.
# Proteins, 34(1), 96-112 (1999)
#
from MMTK import *
from MMTK.Proteins import Protein
from MMTK.NormalModes import EnergeticModes
from MMTK.ForceFields import CalphaForceField
from MMTK.Field import AtomicVectorField
from MMTK.Database import PDBPath
from Scientific.Visualization import Chimera
import chimera
# Load the molecule into Chimera
filename = PDBPath("insulin.pdb")
chimera.runCommand("open pdb:%s" % filename)
# Create a simulation universe containing the protein
universe = InfiniteUniverse(CalphaForceField())
universe.addObject(Protein(filename, model='calpha'))
# Calculate normal modes
modes = EnergeticModes(universe)
# Create the vector field corresponding to the first non-zero mode
# using a grid spacing of 0.5 nm.
field = AtomicVectorField(universe, 0.5, modes[6])
# Create graphics objects for the vector fields.
# The arrows are yellow and their lengths are multiplied by 80.
# Only displacement vectors of lengths between 0. and 0.01 will be shown.
# (This restriction is not necessary for this example, but used for
# illustration.)
graphics = field.graphicsObjects(color='yellow',
scale=80., range=(0., 0.01),
graphics_module=Chimera)
# Display in Chimera. The scale factor is necessary because MMTK
# uses nm whereas Chimera works in Angstrom.
Chimera.Scene(graphics, name="first mode",
scale=1./Units.Ang).view()
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