Cavity programs: Difference between revisions

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[[Image:Jmol-cavities-6zgi-1.4-10.png|200px]]

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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, 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 Cavities''' (buried cavities; voids) are depicted as closed isosurfaces.

[[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 (illustrated here); '''Interior Cavities''' (buried cavities; voids) are depicted as closed isosurfaces (illustrated here: yellow).

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.

Cavity programs: Difference between revisions

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@@ Line 85: / Line 85: @@
 [[Image:Jmol-cavities-6zgi-1.4-10.png|200px]]
 </td></tr></table>
-[[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 Cavities''' (buried cavities; voids) are depicted as closed isosurfaces.
+[[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 (illustrated here); '''Interior Cavities''' (buried cavities; voids) are depicted as closed isosurfaces (illustrated here: yellow).
 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.