Re: [Jmol-users] polyhedra commands

[Sinasi Ellialtioglu]

Beautiful, just what I wanted. Thanks Michael, thanks Bob. Sinasi Miguel wrote: can you remind us of the command for that? Polyhedra are constructed using the selected set of atoms as the centers. Either bond connectivity or distance can be used to specify the vertices. If you specify distance then you can also specify a set of atoms that are valid as the vertices. This set of valid vertex atoms must be specified in parentheses. (I don't recall, but I don't think this vertex-set selection works for 'polyhedra bonds'). If you have exactly 4 vertices and the center is on the inside of the 4 planes formed by those vertices then you become a tetrahedron. If you have exactly 6 vertices and you are on the correct side of the planes formed by those vertices then you become an octahedron. Change color on the selected polyhedra. color polyhedra hotpink Making the polyhedra translucent is valuable because you can see the atoms inside the polyhedra. color polyhedra translucent orange You can explicitly make the edges stand out a bit more to emphasize the polyhedra. You can either turn on all the edges, or only the front edges polyhedra edges|frontedges|noedges Showing only the front edges may help when using translucent polyhedra. load "samples/crystals/kaolinite_small.mol" #turn on polyhedra based upon bond connectivity polyhedra bonds select atomno > 75 # change the color of some color polyhedra blue select atomno > 50 && atomno < 100 # make some translucent color polyhedra translucent yellow polyhedra frontedges load samples/crystals/kaolinite_big_noconnect.pdb # make polyhedra where aluminum is at the center select aluminum # and oxygens within 2.0 angstroms are at the vertices polyhedra 2.0 (oxygen) Miguel ------------------------------------------------------- This SF.Net email is sponsored by Oracle Space Sweepstakes Want to be the first software developer in space? Enter now for the Oracle Space Sweepstakes! http://ads.osdn.com/?ad_idt12&alloc_id344&opÿick _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users