When you import from the CellDesigner sample M_phase.xml, pretty much all nodes except the process nodes go into the single compartment but not the process nodes. If there is no direct way to infer this from CD file, one could check the substrates and products of each process and if they all belong to the same compartment, the process could also be placed there.
When you import from the CellDesigner sample M_phase.xml, pretty much all nodes except the process nodes go into the single compartment but not the process nodes. If there is no direct way to infer this from CD file, one could check the substrates and products of each process and if they all belong to the same compartment, the process could also be placed there.