Cavity programs: Difference between revisions
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[[Jmol]] can identify and display pockets and cavities as isosurfaces. Examples are shown at [[Jmol/Cavities pockets and tunnels]], where you will also find explanations of the interior cavity and pocket commands. Cavities are identified as spaces between macromolecule atoms large enough to accomodate a ''cavity probe'' (default cavity probe radius 1.2 Å), or pockets between a smoothed macromolecular surface (default surface probe radius 10 Å) and atoms of the macromolecule. | [[Jmol]] can identify and display pockets and cavities as isosurfaces. Examples are shown at [[Jmol/Cavities pockets and tunnels]], where you will also find explanations of the interior cavity and pocket commands. Cavities are identified as spaces between macromolecule atoms large enough to accomodate a ''cavity probe'' (default cavity probe radius 1.2 Å, configurable), or pockets between a smoothed macromolecular surface (default surface probe radius 10 Å, configurable) and atoms of the macromolecule. Starting point(s) are not relevant. '''Pockets''' are depicted with open mouths; '''Interior Caviies''' are depicted as closed isosurfaces. | ||
Jmol has an extensive command language that provides great flexibility in visualizing cavities. However, displaying more than one isosurface fragment at a time, and coloring the fragments differently (as in the left snapshot) is cumbersome. | Jmol has an extensive command language that provides great flexibility in visualizing cavities. However, displaying more than one isosurface fragment at a time, and coloring the fragments differently (as in the left snapshot) is cumbersome. | ||
