Scripts: mean_distance.py

#
# Compute mean position of each atom in an ensemble and assign an atom attribute for each atom
# in each ensemble model giving its distance to the mean. This is to allow coloring atoms by
# distance from the mean structure.
#
# This script takes all open molecules as the ensemble and assigns atom attribute distance_from_mean.
#
# Example commands for coloring:
#
# open 1mtx
# show
# open mean_distance.py
# rangecolor distance_from_mean 0 blue 3 white 6 red
#
# Menu Tools / Depiction / Render by Attribute can be used to do coloring and see a histogram of distances.
#

from chimera import openModels, numpyArrayFromAtoms, Molecule
mlist = openModels.list(modelTypes = [Molecule])
ave_xyz = None
for m in mlist:
    mxyz = numpyArrayFromAtoms(m.atoms, xformed = True)
    if ave_xyz is None:
        ave_xyz = mxyz.copy()
    else:
        ave_xyz += mxyz
ave_xyz /= len(mlist)

from numpy import sqrt
for m in mlist:
    mxyz = numpyArrayFromAtoms(m.atoms, xformed = True)
    dxyz = mxyz - ave_xyz
    d = sqrt((dxyz*dxyz).sum(axis=1))
    for a,d in zip(m.atoms, d):
        a.distance_from_mean = d