Molecular Replacement


One of the biggest problems in crystallography is the phase problem, hence the use of experimental phasing. An alternative approach, which is increasingly popular, is the use of known structures to solve the phase problem. This approach is called molecular replacement - a model, very similar in structure to the one crystallized, is computationally placed in the crystallographic unit cell. From this model, phases can be calculated and used to start the process of interpreting the electron density map.


In Phenix the primary program for performing molecular replacement is Phaser. This requires experimental diffraction data, an atomic model(s), the sequence of the molecule in the crystal and typically some estimate of the number of molecules in the crystal. Phaser uses maximum likelihood algorithms to determine the rotation of the model(s) with respect to the unit cell, and then the translation of the rotated model(s) within the unit cell. The output of this process, if successful, is a PDB file containing the placed model(s) and an MTZ file containing coefficients for the electron density made using the placed model(s) and the observed experimental amplitudes. For an introduction to molecular replacement in Phenix, click here.

How to use the Phaser GUI in Phenix: Click here

Common issues

Related programs

Phenix reference manual for Phaser.