Hi Danilo, I'll answer you on the Phenix mailing list! All the best, Tom T On Nov 25, 2013, at 8:14 AM, Danilo Belviso wrote:
> Dear all, > > I am working on a membrane protein covalently bound to a molecular antanna: > it is known that this molecule binds to lysine residue but I do not know how > many and which lysine residues it binds. 20 diffraction datasets of this > 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 am using 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) > > Strangely, no ligand is found at the end of the process even reducing > ligand_cc_min to 0.01. I have run the same command by using an other protein > where an other ligand has been correctly fitted but, also in this case, no > ligand has been detected. Conversely, without the use of ligand_start, > ligandfit properly localizes the ligand. > > I'm doing some mistake in the use of ligand_start? Do you know an other tool > to perform a ligand fitting in these conditions? > > Thanks for your answers. > > Danilo
