Channel Mapping

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Macromolecular crystals are ordered arrays of macromolecules, but are also porous materials. Pore architecture is important for diffusion of ligands and other molecules into and out of crystals, as well for as the response of the crystals to changes in temperature (important for cryocooling).  Although several pieces of software exist for describing surface, pockets and channels in single proteins, none are designed specifically for protein crystals. Map_channels was thus written with two aims in mind: first, to provide straightforward visualization of pores and second, to characterize the pores with metrics relevant for diffusion inside the crystals.

Map_channels carries out two primary functions:

1. Generation of a distance map that can be displayed to gain an intuitive feel for the solvent channels. This is a straightforward calculation in which the unit cell is divided into a grid, and the shortest distance from each grid point to any protein atom in the crystal is calculated. The result is a 3D scalar field of distances to protein. This is written as a ccp4 format map than can be displayed, manipulated and contoured in Coot, Pymol and the like.  An example is shown below:

                Channel Comparison
2. Characterization of the distance map. The distance map is searched for connectivity to identify channels running continuously across the unit cell. Groups, or clusters, of connected gridpoints are analyzed with metrics such as pore radius, tortuosity, width variation and anisotropy.


See: Juers & Ruffin, J. Appl. Cryst. (2014). 47, 2105-2108


Map_channels (includes COOT plugin):