1,330
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Phenix: Difference between revisions
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→Fix His/Asn/Gln sidechain orientations
| Line 340: | Line 340: | ||
Use | Use | ||
phenix.refine data.hkl model.pdb main.nqh_flips=True | phenix.refine data.hkl model.pdb main.nqh_flips=True | ||
to automatically flip these sidechains to make them better fit the density and/or hydrogen bonding pattern. | to automatically flip these sidechains to make them better fit the density and/or hydrogen bonding pattern. | ||
==== [http://www.phenix-online.org/documentation/refinement.htm#anch30 Using a reference model] ==== | |||
A good idea if refinement is done at low resolution but a high resolution model is available. | |||
phenix.refine data.hkl model.pdb main.reference_model_restraints=True reference_model.file=reference.pdb | |||
Use reference_model.sigma=0.5 to tighten the restraints (default 1.0 Angstrom), and use reference_model.limit=30 to enlarge the limit (default 15 degrees) up to which the reference torsion angle will be used. | |||
=== Real-space refinement === | === Real-space refinement === | ||