[phenixbb] Tracing and refining b-strands at 3.3A resolution

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Tue Aug 25 17:39:05 PDT 2009


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
  }
}



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