Scripts: varbond.py

noBond = 3.5
fullBond = 2.0
resIDs = ["57.A", "68.A"]
atomNames = ["SG", "N"]

from chimera import openModels, Molecule, Bond
bondRepr = Bond.Stick
fullRadius = 0.2

atoms = []
allAtoms = openModels.list(modelTypes=[Molecule])[0].atoms
for resID, atomName in zip(resIDs, atomNames):
        for a in allAtoms:
                if str(a.residue.id) == resID:
                        atoms.append(a.residue.atomsMap[atomName][0])
                        break

a1, a2 = atoms
dist = a1.coord().distance(a2.coord())

if dist >= noBond:
        if a1 in a2.neighbors:
                a1.molecule.deleteBond(a1.bondsMap[a2])
else:
        if a1 not in a2.neighbors:
                b = a1.molecule.newBond(a1, a2)
                b.drawMode = bondRepr
        else:
                b = a1.bondsMap[a2]
        if dist <= fullBond:
                b.radius = fullRadius
        else:
                b.radius = fullRadius * (1.0 - (dist-fullBond) / (noBond-fullBond))