getEndNormals (
        c0,
        c1,
        c2,
        )

displayStrands (
        mol,
        color,
        fixedWidth,
        width,
        fixedThickness,
        thickness,
        split,
        splitRatio,
        )

minimizeTwist (
        d,
        nn,
        nb,
        on,
        ob,
        )

showTurn (
        turn,
        color,
        width,
        thickness,
        )

Create a VRML node representing a turn

showHelix (
        helix,
        color,
        fixedRadius,
        radius,
        split,
        splitRatio,
        )

Create a VRML node representing a helix

findTurns ( mol )

findHelices ( mol )

Find helices and sheets in model

addEdges (
        edges,
        offsets,
        coord,
        normal,
        binormal,
        )

determinant ( mat )

deinitialize ()

initialize ()

initialize and deinitialize are called before and after calls to displayHelices, displayStrands and displayTurns. displayTurns should be called last because it uses data populated by the first two routines.

splitResidues ( residues,  atomNames )

Split a list of residues by finding the pair that has the most divergent axes

matrixNormalize ( m )

Chimera is very picky about its matrices

Routine below normalizes a 3x3 matrix to the acceptable tolerance

displayTurns (
        mol,
        color,
        width,
        thickness,
        )

getInteriorNormals (
        c0,
        cb,
        ca,
        )

parametricVars (
        base,
        axes,
        c,
        )

Compute the parametric variables from "base" to "c" using orthonormal bases of "axes"

displayHelices (
        mol,
        color,
        fixedRadius,
        radius,
        split,
        splitRatio,
        )

findStrands ( mol )

showStrand (
        strand,
        color,
        fixedWidth,
        width,
        fixedThickness,
        thickness,
        split,
        splitRatio,
        )

Create a VRML node representing a sheet

findAxes ( resList,  atomNames )

Calculate orthonormal basis vectors from the eigenvectors of the moment of inertia tensor of a set of coordinates

moment of inertia tensor components for an atom are: I[i,j] = mass (r r * delta[i,j] - r[i] * r[j] where r = vector from center of mass to this atom delta = delta function (1 if i == j, 0 otherwise) See Kroto, H.W., Molecular Rotation Spectra, John Wiley and Sons, 1975, p 19 or http://www.phys.ufl.edu/~avery/course/3062_f96/home4/home4.htm