def createOutputStep(self):
inputVol = self.inputStructure.get()
samplingRate = inputVol.getSamplingRate()
volume = Volume()
volume.setFileName(self._getExtraPath("pseudoatoms_approximation.vol"))
volume.setSamplingRate(samplingRate)
x, y, z = volume.getDim()
xv, yv, zv = inputVol.getOrigin(force=True).getShifts()
t = Transform()
t.setShifts((x / 2. * samplingRate) - xv, (y / 2. * samplingRate) - yv,
(z / 2. * samplingRate) - zv)
volume.setOrigin(inputVol.getOrigin())
self._defineOutputs(outputVolume=volume)
self._defineSourceRelation(self.inputStructure.get(), volume)
pdb = AtomStruct(self._getPath('pseudoatoms.pdb'), pseudoatoms=True)
pdb.setVolume(volume)
pdb.setOrigin(t)
self.createChimeraScript(inputVol, pdb)
self._defineOutputs(outputPdb=pdb)
self._defineSourceRelation(self.inputStructure, pdb)
