1,330
edits
Phenix: Difference between revisions
Jump to navigation
Jump to search
→Hydrogens
(→Refinement with mmtbx.lockit: remove) |
|||
| Line 263: | Line 263: | ||
==== Hydrogens ==== | ==== Hydrogens ==== | ||
Use phenix.ready_set to add hydrogens to your PDB file, and (except at ultra-high resolution) | Use phenix.ready_set to add hydrogens to your PDB file, and use (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. | ||