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
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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