Density Modification

Why

The crystallographic phase problem can be solved using experimental phasing or molecular replacement. In both cases the initial phases may be inaccurate because of 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 crystals. In the case of single wavelength (SAD) or single derivative (SIR) data this step in 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 modification of the electron density to conform to prior expectations. The result of this procedure should be a better set of phases, that can be used to make a map for interpretation (i.e. model building).

How

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.

Tutorial on density modification : Click here

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

Common issues

• None

Related programs

• phenix.density_modification: This program performs iterative phase improvement with Resolve density modification, including the use of NCS symmetry and electron-density distributions.
• phenix.multi_crystal_average: This program performs iterative phase improvement by density modification, including averaging electron density, both within a crystal and between crystals. This is a very powerful technique that can generate high quality phases in some circumstances.
• phenix.ncs_average: This program can be used to average the electron density for molecules related by non-crystallographic symmetry (i.e. when multiple copies of the same molecule are present in the asymmetric unit). 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.