I have got the output result files for a protein-ligand docking job submitted in the SwissDock server. Now, I would like to save the structure of the complex for which the ligand has the highest free energy of binding.

However I am unable to do that using UCSF Chimera. How should I do it ? In my case I am doing Save as PDB -> Select atoms -> Save , but only the ligand is being saved, even though I can see the protein.

Please help.