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:
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.
