Jmol/Cavities pockets and tunnels: Difference between revisions
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*You want to show both closed interior cavities and open-mouthed surface pockets. | *You want to show both closed interior cavities and open-mouthed surface pockets. | ||
*You want to show multiple pieces of a single isosurface. | *You want to show multiple pieces of a single isosurface. | ||
At present, Jmol can show only one piece of an isosurface. For example, above are shown three pocket entrances to the interior chamber of the spike protein cavity. Each pocket is displayed with an <tt>isosurface set <integer></tt> command. But only one can be shown at a time. To display all 3, the JVXL file (see below) must be loaded 3 times, giving each a different ID, and then one pocket displayed from each. To also display the interior closed chamber, a 4th isosurface must be loaded. Below are scripts illustrating this. | At present, Jmol can show only one piece of an isosurface. For example, [[#Increasing the Cavity Probe Radius|above are shown three pocket entrances]] to the interior chamber of the spike protein cavity. Each pocket is displayed with an <tt>isosurface set <integer></tt> command. But only one can be shown at a time. To display all 3, the JVXL file (see below) must be loaded 3 times, giving each a different ID, and then one pocket displayed from each. To also display the interior closed chamber, a 4th isosurface must be loaded. Below are scripts illustrating this. | ||
===Preparing PNGJ Files With Cached Isosurfaces=== | ===Preparing PNGJ Files With Cached Isosurfaces=== | ||