Jmol/Cavities pockets and tunnels: Difference between revisions
Eric Martz (talk | contribs) No edit summary |
Eric Martz (talk | contribs) No edit summary |
||
| Line 103: | Line 103: | ||
==Large Cavity Example== | ==Large Cavity Example== | ||
Jmol is unable to produce isosurfaces representing cavities whose interior diameters exceed the maximum diameter of Jmol's envelope probe, 20 Å. As an example, consider OprM of ''Pseudomonas aeruginosa''. This bottle-shaped integral membrane protein is believed to function as the drug discharge duct across the outer membrane<ref name="1wp1">PMID: 15507433</ref>. The [[biological assembly]] of [[1wp1]] has pocket with a single mouth, about 110 Å deep. The inside diameter of this pocket varies from a bit less than 20 Å to about 27 Å. Jmol can, of course, make an isosurface over the entire "bottle", inside and out (command: <tt>isosurface minset 1000 solvent 2.0</tt>, shown here in cross section with the protein in sticks (wireframe): | Jmol is unable to produce isosurfaces representing cavities whose interior diameters exceed the maximum diameter of Jmol's envelope probe, 20 Å. As an example, consider OprM of ''Pseudomonas aeruginosa''. This bottle-shaped integral membrane protein is believed to function as the drug discharge duct across the outer membrane<ref name="1wp1">PMID: 15507433</ref>. The [[biological assembly]] of [[1wp1]] has pocket with a single mouth, about 110 Å deep. The inside diameter of this pocket varies from a bit less than 20 Å to about 27 Å. Jmol can, of course, make an isosurface over the entire "bottle", inside and out (command: <tt>isosurface minset 1000 solvent 2.0</tt>), shown here in cross section with the protein in sticks (wireframe): | ||
[[1wp1-solvent-surface-slab.png| | <br>[[Image:1wp1-solvent-surface-slab.png|300px]] | ||
</StructureSection> | </StructureSection> | ||