Phenix: Difference between revisions

2,041 bytes added ,  26 January 2012
(→‎Validation: phenix.r_factor_statistics)
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See the [http://www.phenix-online.org/documentation/refinement.htm#anch26 documentation].
See the [http://www.phenix-online.org/documentation/refinement.htm#anch26 documentation].
==== DEN refinement (similar to what is in CNS) ====
DEN restraints can be activated in phenix.refine from the
command-line with the current version and latest nightly builds, and
they are the same deformable elastic network restraints available in
CNS. PHENIX developers have been working closely with Axel Brunger and Gunnar
Schroder to implement DEN in Phenix.
They have not yet officially announced the DEN restraints as they are
still being tested and actively developed to get the implementation
just right, and the parameterization is still very much in flux. It is
hoped that by the next version it will become and a stable feature, and
at that point DEN will be added as an option in the GUI.
These restraints have been shown to be particularly useful at low
resolution, and there has been success in using at 4-5A and below. It is unclear
how useful they would be at relatively high resolution (say
2.5A or higher), as there are other restraint methods that work well
at that resolution range that are far less computationally intensive.
In almost all cases it is best to optimize the gamma and weight
parameters, which is quite time intensive but is most likely to give
the best results. Currently this can be parallelized, but only on
cores that share memory. If you do optimize the
gamma and weight parameters, you cannot simultaneously optimize B
factor weights, which is another limitation that will be overcome in
the future.
As soon as a stable version is announced in the context of a new
release, documentation will be available.
To use DEN with the current release (1.7.3), you can use a
parameterization such as this:
refinement {
  main {
  den_refinement = True
  number_of_macro_cycles = 1
  nproc = 8
  }
  refine {
  strategy = *individual_sites individual_sites_real_space rigid_body \
              *individual_adp group_adp tls occupancies group_anomalous
  }
  den {
  reference_file = reference.pdb
  optimize = True
  annealing_type = *torsion cartesian
  final_refinement_cycle = True
  }
}


==== TLS ====
==== TLS ====
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