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A computation tool is described that facilitates visualization and characterization of solvent channels or pores within macromolecular crystals. A scalar field mapping the shortest distance to protein surfaces is calculated on a grid covering the unit cell and is written as a map file. The map provides a multiscale representation of the solvent channels, which when viewed in standard macromolecular crystallographic software packages gives an intuitive sense of the solvent channel architecture. The map is analysed to yield descriptors of the topology and the morphology of the solvent channels, including bottleneck radii, tortuosity, width variation and anisotropy.
Supporting information
 | Quicktime video file https://doi.org/10.1107/S160057671402281X/jo5006sup1.mov
Movie S1 illustrating the multiscale aspect of the solvent channels in 8tln that can be viewed with the distance map. The c axis runs up-down. Channels are shown in blue, and a single protein is shown in ribbons representation at the bottom of the figure. The view is rotated about the c axis one complete revolution, and then the contour level is increased. 12.5 Å contour level – there is one helical pore per unit cell (four pores are visible in the figure). 10.0 Å contour level – the helical pore is larger, and a few smaller pockets can be seen. 7.5 Å contour level – the pockets have nearly fused to give the second helical channel. 5.0 contour level – the second helical channel can be seen. Additionally, there is nearly connectivity horizontally across the figure – in the a and b directions. |
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