Model Building

Why

Determining the structure of a macromolecule typically requires building an atomic model by fitting to maps obtained from experimental phasing or molecular replacement. For many cases, automated methods can be used to build models for both proteins and nucleic acids.

The accuracy and completeness of the 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 built, which require manual completion.

How

In Phenix, several programs aid in automated model building; the main one is phenix.autobuild. The model building process integrates phase improvement using density modification methods with automated map interpretation in order to build and refine models. This minimally requires an experimental density map, experimental diffraction data, and the sequence of the molecule(s) in the crystal. The program outputs a PDB file with the automatically built model and the map coefficients for the best electron density map created during the model building process.

How to use the phenix.autobuild GUI: Click here

Common issues

Related programs

Phenix reference manual for phenix.autobuild