Structure Refinement

Why

Once an atomic model has been built into an electron density map, or obtained by molecular replacement, it needs to be optimized to best fit the experimental data while also preserving good agreement with prior chemical knowledge. This process is typically iterated with manual model rebuilding, making use of improved electron density maps, created by including phase information from the current atomic model.

How

The primary program for refinement of atomic models in Phenix is phenix.refine. This applies optimization algorithms (minimization or simulated annealing) to change the parameters of the model, typically coordinates and atomic displacement parameters, to improve the fit of the model to the data. At the same time restraints to prior chemical information, e.g. bond lengths, angles, torsions, are also applied in order to maintain good stereochemistry.

How to use the phenix.refine GUI: Click here

Common issues

• Frequently asked questions for structure refinement

Related programs

• phenix.rosetta_refine: This program combines crystallographic structure refinement algorithms from Phenix with physically realistic potentials for model optimization from Rosetta. This is intended for use in difficult cases, especially at low resolution where it combines a wide radius of convergence to the correct structure with excellent geometry.
• phenix.ensemble_refinement: This program uses molecular dynamics as a mechanism to generate conformations of molecules in the crystal. A time averaging method is used to generate ensemble models fitted to diffraction data. These ensemble models can contain ~50-500 individual structures and simultaneously account for anisotopic and anharmonic atomic distributions.
• ERRASER: Another Rosetta method that performs real-space rebuilding of RNA structures for improved geometry and fit to data.

Phenix reference manual for phenix.refine