Molecular Replacement


One of the biggest challenges in crystallography is the phase problem, which can be addressed with experimental phasing methods. A popular alternative approach is molecular replacement (MR), which uses known structures to solve the phase problem. When a structurally similar model (e.g., a homologue) is available, this model is computationally placed in the unit cell containing the unknown structure. An initial electron density map is then calculated with the phases from the homologue and the observed structure factors.

The success of MR calculations depends on how much signal can be extracted from the data using the particular model, which in turn depends on a combination of the model quality and completeness, data resolution, and number of diffraction observations. For crystals of medium-sized proteins diffracting to moderate resolution, for example, the sequence identity between the molecule and homologue should be >25-30% and the r.m.s. deviation between C⍺ atoms should be <2.0 Å.


In Phenix, the primary program for performing molecular replacement is Phaser. This requires experimental diffraction data, 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 model 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

Phenix reference manual for Phaser.

Common issues

Related programs