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Phenix: Difference between revisions
→Ligands
(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. | phenix.ready_set model.pdb | ||
will produce | will produce model.updated.pdb and model.ligands.cif, which may be fed to phenix.refine by | ||
phenix.refine model.pdb data.mtz | 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. | ||