Density Modification

Why

The crystallographic phase problem can be solved using experimental phasing or molecular replacement. In both cases, these initial phases may be inaccurate due to experimental errors, low signal-to-noise, or model bias. Therefore, it is usually necessary to improve the phases by exploiting our prior knowledge about electron density distributions in the crystal. In the case of single wavelength (SAD) or single derivative (SIR) data, this step is essential for resolving the inherent phase ambiguity in these experiments.

The phase improvement procedure is usually referred to as density modification because new phase estimates are obtained by modifying the electron density to conform to prior expectations. For example, methods to improve phases include solvent flattening, histogram matching, and non-crystallographic symmetry averaging (if NCS is present). The result of the procedure should be a better set of phases, which can be used to make a map for interpretation (i.e., model building).

How

In Phenix, several programs carry out density modification (see the list of Related programs below). Density modification can be performed using either a set of experimental phases (i.e., Hendrickson-Lattmann coefficients) or experimental amplitudes and an atomic model (from which the phases are calculated). The density modification program will try to automatically determine solvent content and non-crystallographic relationships between regions of density.

How to use the phenix Resolve density modification GUI: Click here

Tutorial on density modification : Click here

Related programs

• phenix.density_modification: This program performs iterative phase improvement with Resolve density modification, including the use of non-crystallographic symmetry and electron-density distributions.
• phenix.multi_crystal_average: This program improves phases interactively and averages electron density, both within a crystal and between crystals. This very powerful technique can generate high quality phases in some circumstances.
• phenix.ncs_average: This program averages the electron density for molecules related by non-crystallographic symmetry. No iterative phase improvement is performed, just a single round of averaging. This is useful for improving signal-to-noise in maps for model building.