Jmol/Cavities pockets and tunnels: Difference between revisions
Eric Martz (talk | contribs) No edit summary |
Eric Martz (talk | contribs) No edit summary |
||
| Line 44: | Line 44: | ||
It is revealing to color this cavity by distance from the surface with this command: | It is revealing to color this cavity by distance from the surface with this command: | ||
:<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><ref>This command works only if a previous <tt>isosurface ... cavity</tt> command has been run in the same session. It will not work if the surface is loaded from a JVXL file alone, because then the surface has not been defined.</ref> <!--6zgi-m1000-cav-sd-set2.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--> | <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--> | ||