Hi Gino,
So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement?
Nope. But you could use the custom bond definitions to restrain hydrogen bonds. The syntax is explained in the phenix.refine documentation; an example is below. The main trouble is that we don't have an automatic tool to generate the bond restraints for you. Maybe others have suggestions how to use external programs? Ralf refinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = "chain G and resname ASP and resid 20 and name N" atom_selection_2 = "chain G and resname GLY and resid 33 and name O" symmetry_operation = None distance_ideal = 2.8 sigma = 0.1 slack = 0.3 } bond { action = *add delete change atom_selection_1 = "chain G and resname GLY and resid 33 and name N" atom_selection_2 = "chain G and resname SER and resid 21 and name O" symmetry_operation = None distance_ideal = 2.8 sigma = 0.1 slack = 0.4 } }