Structure Refinement


Once an atomic model has been built into an electron density map, or obtained by molecular replacement, you need to optimize it to best fit the experimental data while also preserving good agreement with prior chemical knowledge.

For crystallographic data, this refinement process is usually done in reciprocal space. Using a least-squares or maximum-likelihood target, the model parameters are changed so the model-derived structure factors match the amplitudes or intensities of the experimental structure factors. For example, these model parameters can include (a) atomic parameters, such as coordinates, atomic displacement parameters, occupancies, and scattering factors, and (b) non-atomic parameters that describe contributions from bulk solvent, twinning, and crystal anisotropy.


In Phenix, the primary program for refining atomic models is phenix.refine. This applies optimization algorithms (minimization or simulated annealing) to change the model parameters (typically coordinates and atomic displacement parameters) to improve the fit of the model to the data. At the same time, it applies restraints to prior chemical information (such as bond lengths, angles, and torsions) to maintain good stereochemistry. This customizable program allows multiple refinement strategies to be combined and applied to any selected part of the model in a single run.

How to use the phenix.refine GUI: Click here

Phenix reference manual for phenix.refine

Common issues

Related programs