symmetric docking uses the minimal subsystem during docking. The output contains also the smallest subsystem. For example, in a C17 system (3kml), only three neighboring subunits are used in docking and the output decoys contain also only three subunits (DiMaio2011, PLoS ONE). How to reconstruct the complete system based on the output? It seems the original symmetric definition file can not be relied on any more.
My guess is to apply make_symmdef_file.py to generate new SDF for each docking decoy and transform the decoy according to the new SDF. Are there official way/script for doing this?