Phenix: Difference between revisions

Phenix (edit)

Revision as of 22:13, 26 January 2012

2,041 bytes added , 26 January 2012

→‎Low resolution refinement

Kay

Bureaucrats

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 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
+.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 ====