Dear all, I am working on a membrane protein bound to a antenna molecule: I know that the molecule binds to lysine residue but I do not know how many and which lysine residues it binds. 20 diffraction datasets of protein-ligand complex have been obtained and now, I would quickly localize the ligand using the Fo-Fc map of each data set and using the information on the covalent bound protein-ligand. Ligandfit tool (PHENIX) seems to be indicated to do this; to use the information on the covalent bound, I have thought to use the ligand_start keyword with a pdb containing a ghost atom (however present in ligand model) perfectly superposed to the lysine atom that should bind the ligand. The command used is: phenix.ligandfit data=prot.mtz model=prot.pdb ligand=lig.pdb ligand_start=lig_start.pdb input_labels="FOFCWT PHFOFCWT" \ refine_ligand=True \ nproc=32 \ cif_def_file_list=lig.cif description: - prot.mtz (data) - prot.pdb (protein without ligand) - lig.pdb (ligand containing ghost atom) - lig_start.pdb (ghost atom superpose to NZ of a lysine) - lig.cif (restrain of lig.pdb) At the end of the processing, ligand is not found. So, I have tryed with ligand_cc_min=0.01, but also in this case ligandfit does not give result. I have thought that no ligand is present. However, to be sure that all was correct, I have run the same command by using an other protein where an other ligand has been correctly fitted. Also in this case, no result has been obtained. Conversely, without the use of ligand_start, ligandfit properly localizes the ligand. I'm doing some mistake in the use of ligand_start? Thanks for your answers. Danilo