Phenix: Difference between revisions

9 bytes added ,  9 May 2019
(link to phenixBB added)
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   definitions for unknown ligands.
   definitions for unknown ligands.
In that case, just running
In that case, just running
  phenix.elbow model.pdb --do-all --output=all_ligands
  phenix.ready_set model.pdb  
will produce all_ligands.cif, which may be fed to phenix.refine by
will produce model.updated.pdb and model.ligands.cif, which may be fed to phenix.refine by
  phenix.refine model.pdb data.mtz all_ligands.cif ...
  phenix.refine model.updated.pdb data.mtz model.ligands.cif ...
If no PDB file for a ligand is available, its SMILES string should be input to phenix.elbow, and phenix.ready_set should run to generate the LINK records (e.g. for a non-natural amino acid that is part of the polypeptide chain), using phenix.elbow's CIF file.
If no PDB file for a ligand is available, its SMILES string should be input to phenix.elbow, and phenix.ready_set should run to generate the LINK records (e.g. for a non-natural amino acid that is part of the polypeptide chain), using phenix.elbow's CIF file.


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