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?
contacted Ingemar offline and his answer is:
“What I do is I run the make_symmdef_file.pl on it and make sure it detects neighbors really far away (-r 200 or something). that creates the full ring as NAME_OF_MY_MODEL_symm.pdb.”
I am modeling an helix assembly and I was wondering how to reconstruct the assembly from SymDock output pdb. The output only includes the chains that are in direct contact with the master subunit, and hence I don’t have the next chain along the fiber/helix to include in the command line (make_symmdef_file.pl)