Ralf et al. My question with this approach is that is there any potential to have a negative effect on refining the structure, given that one is introducing a number of bonds with relatively high average deviations from the mean ? The rest of the bonded (covalent) geometry has an rms in the range 0.004 - 0.015 (-ish) but this is one to two orders of magnitude tighter than a hydrogen bond. Is the target function sophisticated enough to handle this or is there a problem with treating hbonds and covalent bonds as peers ? Phil Jeffrey Princeton Ralf W. Grosse-Kunstleve wrote:
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 } } _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb