Smith If you have the Mg in the PDB model with MG as the atom name, residue name and element you don't need to do anything more. For ligands, eLBOW takes a wide variety of inputs and PDB is the least useful. I recommend SMILES, Mol3D and/or SDF. If it's known ligand from Ligand Expo, then you can use eLBOW thus phenix.elbow --chemical-component=XYZ to get a restraints file and a PDB file. You'll need a set of restraints for each ligand but they can be combined into one file using elbow.join_cif_files usage: elbow.join_cif_files merge1 merge2 ... target Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Sep 30, 2015 at 8:31 AM, Smith Liu wrote:

Dear All,

If my protein contains a metal ion (Mg2+ for example, do I need a cif for the metal for phenix.refine? If my protein contains another ligand, which server can produce the ligand PDB suitable for the eLBOW? If my protein contains 2 ligands, then do I need 2 cif files for the phenix.refine or the phenix.real_space_refine?

I am looking forward to getting your reply.

Best regards.

Smith

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