Model Building

Why

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.

How

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

• Frequently asked questions about model building

Related programs

• phenix.find_helices_strands: This program can be used to very rapidly locate protein secondary structure elements in an electron density map. This can be used even at low resolution (4Å or worse). This is extremely useful for quickly confirming that a map contains macromolecular features, or for interpreting low resolution maps. Optionally, the amino acid sequence can be provided and residues will be fitted where density permits.
• phenix.fit_loops: This program can fit loops into protein structures given the current model, the sequence and an electron density map. Model building procedures are sometimes unable to fit models to poor density in loop regions, especially in the initial stages of map interpretation. As the model becomes more complete and maps improve the weaker density in loops regions may become clearer, and thus can be fit using phenix.fit_loops.
• phenix.map_to_model: This is designed for lower resolution model-building. It is suitable for both crystallographic maps and cryo-EM maps. It can take into account symmetry that has been used to create a map, building only the unique part of the model and expanding to the remaining NCS-related copies.
• phenix.erraser: This program uses ERRASER (Enumerative Real-space Refinment ASsisted by Electron-density under Rosetta) to rebuild RNA structures by combining Rosetta and Phenix. By supplementing the Rosetta RNA scoring function with electron-density restraint, ERRASER can confidently reduce the errors in RNA crystallographic models while retaining a good fit to the diffraction data.

Phenix reference manual for phenix.autobuild