[phenixbb] on phenix.refine

Nigel Moriarty nwmoriarty at lbl.gov
Wed Sep 30 08:59:23 PDT 2015


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 merge1 merge2 ... target



Nigel W. Moriarty
Building 33R0349, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Wed, Sep 30, 2015 at 8:31 AM, Smith Liu <smith_liu123 at 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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