Density Modification


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).


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

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