Model Building


The main goal of a crystallographic experiment is to arrive at an atomic interpretation of the electron density in the crystal. This typically requires building an atomic model by fitting to maps obtained from experimental phasing or molecular replacement. For many cases it is possible to use automated methods for building models, for both proteins and nucleic acids. The accuracy and completeness of model building is a function of the quality of the starting electron density map, and less critically the resolution of the data. At low resolution (3.0Å or worse) partial models are usually build, requiring manual completion.


There are a number of programs in Phenix to aid in automated model building, the main one being phenix.autobuild. The process of model building interates phase improvement using density modification methods with automated map interpretation to build models, and model refinement. This minimally requires an experimental density map, experimental diffraction data, and the sequence of the molecule(s) in the crystal. The output will be a PDB file with the automatically built model and map coefficients for the best electron density map created during the process of model building.

How to use the phenix.autobuild GUI: Click here

Common issues

Related programs

Phenix reference manual for phenix.autobuild