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 : NWMoriarty@LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Wed, Sep 30, 2015 at 8:31 AM, Smith Liu <smith_liu123@163.com> 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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