Jmol/Cavities pockets and tunnels: Difference between revisions
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As the cavity probe radius increases, cavities are displayed with less detail. Also, cavities or tunnel connections between cavities that are smaller than the probe may fail to be detected. Recall that the deeper chamber of our membrane-proximal cavity of interest is connected to three entrance pockets by narrow tunnels. As the cavity probe radius increases, those narrow tunnels are no longer detected. At 2.0 Å, two of the entrances are no longer connected to the deeper chamber. At 2.5 Å, none are connected. The cavity probe radius in Å can be added to the end of Jmol's isosurface command like this: | As the cavity probe radius increases, cavities are displayed with less detail. Also, cavities or tunnel connections between cavities that are smaller than the probe may fail to be detected. Recall that the deeper chamber of our membrane-proximal cavity of interest is connected to three entrance pockets by narrow tunnels. As the cavity probe radius increases, those narrow tunnels are no longer detected. At 2.0 Å, two of the entrances are no longer connected to the deeper chamber. At 2.5 Å, none are connected. The cavity probe radius in Å can be added to the end of Jmol's isosurface command like this: | ||
:<tt>isosurface minset 30 cavity | :<tt><scene name='85/858407/6zgi-pocbur_2point5/1'>isosurface minset 30 cavity 2.5</scene></tt><!--6zgi-pocbur2.5 (minset 30)--> | ||
Because the deeper chamber has no entrances from the surface, it will not be shown when the entrance pockets are rendered open with the ''pockets'' modifier. Those open pockets must be combined with a separate isosurface calculation for the ''interior'' chamber. The scripts for doing this are below. | |||
==Large Cavity Example== | ==Large Cavity Example== | ||