When a depiction is created that exceeds the size of the draw area instead of the depiction being scaled to fit within the drawing area the depiction is instead cropped resulting in, for large molecules, significant sections of structure not being visible.
fitToScreen is set to true.
Manually adjusting the scaling using:
renderer.getRenderer2DModel().setScale(double) where renderer is an AtomContainerRenderer has no visible effect.
(the same call with setZoomFactor instead of setScale does work)