Jmol/Cavities pockets and tunnels: Difference between revisions
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:<tt><scene name='85/858407/6zgi-m1000-cav-sd-set2/1'>isosurface map property surfacedistance</scene></tt> <!--6zgi-m1000-cav-sd-set2.pngj--> | :<tt><scene name='85/858407/6zgi-m1000-cav-sd-set2/1'>isosurface map property surfacedistance</scene></tt> <!--6zgi-m1000-cav-sd-set2.pngj--> | ||
<scene name='85/858407/6zgi-m1000-cav-sd-set2-detail/2'>Close examination</scene> shows that the red parts, which are at or near the protein surface, are mostly '''closed'''. The "cavity" command, without modifiers, generates closed isosurfaces. <!--Image:6zgi-m1000-cav-sd-set2-detail.pngj--> | <scene name='85/858407/6zgi-m1000-cav-sd-set2-detail/2'>Close examination</scene><ref>The command for ''close examination'' is based on finding that Asn1107 is close to the deep chamber of the membrane-proximal cavity. The command is <tt>zoomto {1107} 266</tt>. This centers the deep part of the cavity and zooms to 266%.</ref> shows that the red parts, which are at or near the protein surface, are mostly '''closed'''. The "cavity" command, without modifiers, generates closed isosurfaces. <!--Image:6zgi-m1000-cav-sd-set2-detail.pngj--> | ||
===Pockets vs. Interior Cavities=== | ===Pockets vs. Interior Cavities=== | ||