Jmol/Cavities pockets and tunnels
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====Generating Cavity Isosurfaces==== | ====Generating Cavity Isosurfaces==== | ||
The Jmol commands for generating cavity isosurfaces will be found in the [https://chemapps.stolaf.edu/jmol/docs/#isosurfacesurfaceobject--molecular/solventsurfaces Jmol/JSmol Interacive Scripting Documention] under ''isosurfaces: molecular/solvent surfaces''. Near the bottom of that very long section, important commands for after the cavity isosurfaces are calculated: | The Jmol commands for generating cavity isosurfaces will be found in the [https://chemapps.stolaf.edu/jmol/docs/#isosurfacesurfaceobject--molecular/solventsurfaces Jmol/JSmol Interacive Scripting Documention] under ''isosurfaces: molecular/solvent surfaces''. Near the bottom of that very long section, important commands for after the cavity isosurfaces are calculated: | ||
| - | *''isosurface area set (integer)'' reports the surface area of one isosurface in Å<sup>2</sup> | + | *''isosurface area set (integer)'' reports the surface area of one isosurface in Å<sup>2</sup>. |
| - | *''isosurface delete'' | + | *''isosurface delete'' to clear existing isosurfaces before a new calculation. |
*''isosurface set (integer)'' displays just one of the isosurfaces. | *''isosurface set (integer)'' displays just one of the isosurfaces. | ||
*''isosurface set 0'' displays all of the isosurfaces. | *''isosurface set 0'' displays all of the isosurfaces. | ||
| - | *''isosurface volume set (integer)'' reports the volume of one isosurface in Å<sup>3</sup> | + | *''isosurface volume set (integer)'' reports the volume of one isosurface in Å<sup>3</sup>. |
==Small Cavities Example== | ==Small Cavities Example== | ||
</StructureSection> | </StructureSection> | ||
Revision as of 18:45, 11 August 2020
Your Heading Here (maybe something like 'Structure')
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