Scripts: aniso.py

rgba = (1.0, 0.0, 0.0, 1.0)
scale = 1.0

def ellipsoid(surface, center, axes, lengths):
        from Icosahedron import icosahedron_triangulation
        varray, tarray = icosahedron_triangulation(subdivision_levels = 3,
                                                sphere_factor = 1.0)
        from numpy import dot, sqrt
        ee = varray * sqrt(lengths)
        ev = dot(ee, axes)
        ev += center

        surface.addPiece(ev, tarray, rgba)

from chimera import selection, UserError, openModels
atoms = [a for a in selection.currentAtoms() if hasattr(a, 'anisoU')]
if not atoms:
        raise UserError("No ANISOU atoms selected")

perMol = {}
for a in atoms:
        perMol.setdefault(a.molecule, []).append(a)

for m, matoms in perMol.items():
        import _surface
        sm = _surface.SurfaceModel()
        sm.name = "ANISOU for %s" % m
        from numpy.linalg import svd
        for a in matoms:
                ignore, vals, vecs = svd(a.anisoU)
                vals *= scale
                ellipsoid(sm, a.coord(), vecs, vals)
        openModels.add([sm], sameAs=m)