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Phenix: Difference between revisions
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will produce all_ligands.cif, which may be fed to phenix.refine by | will produce all_ligands.cif, which may be fed to phenix.refine by | ||
phenix.refine model.pdb data.mtz all_ligands.cif ... | phenix.refine model.pdb data.mtz all_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 | 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. | ||
== Constraints and restraints in real space == | == Constraints and restraints in real and reciprocal space == | ||
=== | === Hydrogens === | ||
Use phenix.ready_set to add hydrogens to your PDB file, and (except at ultra-high resolution) the riding hydrogen model in phenix.refine (this is the default so you do not have to specify anything). | Use phenix.ready_set to add hydrogens to your PDB file, and (except at ultra-high resolution) the riding hydrogen model in phenix.refine (this is the default so you do not have to specify anything). | ||
phenix.ready_set internally uses phenix.elbow for ligands and phenix.reduce for the protein. phenix.pdbtools can also add hydrogens (FIXME: what are the differences?). | phenix.ready_set internally uses phenix.elbow for ligands and phenix.reduce for the protein. phenix.pdbtools can also add hydrogens (FIXME: what are the differences?). | ||
Hydrogens should not be used in NCS and TLS groups - it might be a good idea to add <font face="Courier"> and not (element H or element D)</font> to all selection strings. | Hydrogens should not be used in NCS and TLS groups - it might be a good idea to add <font face="Courier"> and not (element H or element D)</font> to all selection strings. | ||
See the [http://www.phenix-online.org/documentation/refinement.htm#anch32 phenix.refine documentation]. | |||
=== Occupancy === | === Occupancy === | ||
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You can find more information about secondary structure restraints in the [http://www.phenix-online.org/newsletter/CCN_2010_07.pdf PHENIX Newsletter] (pages 12-17). | You can find more information about secondary structure restraints in the [http://www.phenix-online.org/newsletter/CCN_2010_07.pdf PHENIX Newsletter] (pages 12-17). | ||
=== | === Low resolution refinement === | ||
Use an existing high resolution model (e.g. in a different spacegroup) for restraining the dihedrals: | Use an existing high resolution model (e.g. in a different spacegroup) for restraining the dihedrals: | ||
phenix.refine data.hkl model.pdb main.reference_model_restraints=True reference_model.file=reference.pdb | phenix.refine data.hkl model.pdb main.reference_model_restraints=True reference_model.file=reference.pdb | ||
The behaviour can be modified with the keywords <font face="Courier">reference_model.limit</font> (default 15 degrees) and <font face="Courier">reference_model.sigma</font> (default probably 1 degrees - the current documentation says 1 Angstrom which is probably not right). | The behaviour can be modified with the keywords <font face="Courier">reference_model.limit</font> (default 15 degrees) and <font face="Courier">reference_model.sigma</font> (default probably 1 degrees - the current documentation says 1 Angstrom which is probably not right). | ||
See the [http://www.phenix-online.org/documentation/refinement.htm#anch26 full documentation]. | |||
=== TLS === | === TLS === | ||