Structure Refinement


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.


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

Related programs

Phenix reference manual for phenix.refine