Jmol/Cavities pockets and tunnels
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This generates 212 cavities, ranging in volume from 353 down to 1.9 Å<sup>3</sup>. Comparing this with the initial 2-cavity result (green link above), note that '''neither of the cavities of interest is here.''' The largest cavity here is much smaller than the smaller cavity in the initial result. By trial and error, this appears to be because the cavity probe size is too small. The default probe radius is 1.2Å. The distinction between interior cavities and pockets/tunnels is whether the space intersects with an envelope of the molecule. Such an intersection represents a mouth. The default probe radius for the envelope is 10 Å. Quoting from the [https://chemapps.stolaf.edu/jmol/docs/#isosurface Jmol documentation], "Smaller numbers for the cavity radius lead to more detailed cavities; smaller numbers for the envelope radius lead to cavities that are more internal and extend less toward the outer edge of the molecule." ''A minimum volume of 1.9 Å<sup>3</sup> is puzzling since it is smaller than the volume of the spherical probe: 1.2 Å is the default radius; spherical probe volume is 7.2 Å<sup>3</sup>. At least no negative volumes are reported.'' | This generates 212 cavities, ranging in volume from 353 down to 1.9 Å<sup>3</sup>. Comparing this with the initial 2-cavity result (green link above), note that '''neither of the cavities of interest is here.''' The largest cavity here is much smaller than the smaller cavity in the initial result. By trial and error, this appears to be because the cavity probe size is too small. The default probe radius is 1.2Å. The distinction between interior cavities and pockets/tunnels is whether the space intersects with an envelope of the molecule. Such an intersection represents a mouth. The default probe radius for the envelope is 10 Å. Quoting from the [https://chemapps.stolaf.edu/jmol/docs/#isosurface Jmol documentation], "Smaller numbers for the cavity radius lead to more detailed cavities; smaller numbers for the envelope radius lead to cavities that are more internal and extend less toward the outer edge of the molecule." ''A minimum volume of 1.9 Å<sup>3</sup> is puzzling since it is smaller than the volume of the spherical probe: 1.2 Å is the default radius; spherical probe volume is 7.2 Å<sup>3</sup>. At least no negative volumes are reported.'' | ||
| - | Increasing the cavity probe radius to 2.0 Å still does not display the cavities of interest (not shown). 44 separate cavities are displayed. ''Of concern is that most have volumes much less than the | + | Increasing the cavity probe radius to 2.0 Å still does not display the cavities of interest (not shown). 44 separate cavities are displayed. ''Of concern is that most have volumes much less than the spherical volume of the probe (33.5 Å^3), and it is not clear how a cavity smaller than the probe can be detected. Of further concern is that several cavities report '''negative volumes'''.'' |
Increasing it to 2.6 Å finally displays the smaller cavity of interest, but not the larger. This cavity probe radius gives a volume of 1,855 Å<sup>3</sup> for the smaller of the desired cavities, 16% larger than with the 3.0 Å probe. | Increasing it to 2.6 Å finally displays the smaller cavity of interest, but not the larger. This cavity probe radius gives a volume of 1,855 Å<sup>3</sup> for the smaller of the desired cavities, 16% larger than with the 3.0 Å probe. | ||
</StructureSection> | </StructureSection> | ||
Revision as of 22:47, 13 August 2020
CAUTION: cavity counts and volumes, and scenes of cavities, are provisional. Some inconsistencies noted below in italics suggest that Jmol may have some "isosurface interior cavity" bugs. These are being investigated. Once they are resolved, this notice will be removed. User:Eric Martz, August 13, 2020.
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