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. Author manuscript; available in PMC: 2012 Sep 1.

Published in final edited form as: Methods. 2011 Jul 29;55(1):94–106. doi: 10.1016/j.ymeth.2011.07.005

The phenix.refine GUI uses tabs to collect the different kinds of information required. A) The Input data tab provides fields for files, such as structure factors, coordinates, and additional geometric restraints. The type of file is detected automatically, information extracted, and other fields in the GUI automatically completed when possible (such as space group and unit cell information read from a structure factor file). B) The Refinement settings tab provides fields to control the refinement job. This includes the strategy for the refinement, which is generally the parameterization of the model, use of additional restraints, and other options that influence the refinement. To use simulated annealing in refinement either Cartesian or Torsion angle are selected by use of the check boxes in this tab. To use rigid body refinement the Rigid body check box is selected and the appropriate rigid bodies identified using textual atom selections or graphically using a selection GUI. The same procedure applies to the use of TLS refinement.

The phenix.refine GUI uses tabs to collect the different kinds of information required. A) The Input data tab provides fields for files, such as structure factors, coordinates, and additional geometric restraints. The type of file is detected automatically, information extracted, and other fields in the GUI automatically completed when possible (such as space group and unit cell information read from a structure factor file). B) The Refinement settings tab provides fields to control the refinement job. This includes the strategy for the refinement, which is generally the parameterization of the model, use of additional restraints, and other options that influence the refinement. To use simulated annealing in refinement either Cartesian or Torsion angle are selected by use of the check boxes in this tab. To use rigid body refinement the Rigid body check box is selected and the appropriate rigid bodies identified using textual atom selections or graphically using a selection GUI. The same procedure applies to the use of TLS refinement.