What is volume matching?

Volume matching is the procedure of superimposing one volume on another. This allows us to look for similarities or differences between the two volumes. Whole volumes can be matched with each other, or sub-volumes associated with particular biological components may be mapped. The aim is to compare volume data from different samples, or collected under different conditions.

Superposition of two proteins based on their atomic coordinates is already a common operation, and there are many existing programs and services available. As structural biology moves to considering larger complexes and molecular machines, atomic coordinate models are not always available. Volume matching addresses this scenario. 

The above schematic illustrates what we are trying to achieve. There are a number of methods for aligning two volumes against each other – described later in the methodologies section. Although it may be time-consuming, alignment is relatively straightforward. A harder question to answer is finding out what is the best alignment from several possibilities; this issue is described in the section on scoring functions.

Difference maps

Once two volumes have been matched, and the transformation required to superimpose them determined, a difference map can be calculated. Features occurring in the first map but not the second will appear as positive peaks, while features occurring in the second map but not the first will appear as negative peaks. This means an additional macromolecular component present in one volume will be highlighted as a region of positive peaks. Conformational changes are also highlighted as a pair of positive and negative peaks, representing the new and old positions.

In practice, to get clean difference maps, the range of grid values have to be brought onto the same scale at all spatial frequencies (power spectrum matching).