| Hi All, We have been trying to use Jmol to display coordination polyhedra for a range of inorganic structures and have encountered what seems to us anomalous behaviour. I have set up some of the pages on an external server using Jmol 11.6RC6 so that anyone interested can take a look. These pages are unfinished and may disappear without warning. I suspect some of these may require expert input from Bob but others may sound familiar to other users. 1st "Ni Polyhedron" button why is third octahedron not visible? perhaps the code "restrict cell={2 2 2}; set unitcell {1 1 1}; centre unitcell; polyhedra 6 ((_ni) and visible); colour polyhedra translucent; zoom 200" only works properly when the polyhedra are inside the cells, and not when the polyhedra overlaps into a second cell? Various attempts at showing BOTH the tetrahedra and octahedra for both types of Li. Perhaps problems displaying 2 types of polyhedra of the same element (Li) together (changing colours or translucent/opaque) also, an example where polyhedra do not extend beyond unitcell (notice missing Oh polyhedra on one side) These use code "hideNotselected", to hide unwnated ions but how can we select polyhedra as well so they show up? Then using Jmol.jar to view close-packed structures and hoping to display the holes in ccp, hcp, and bcc (attached) leads to many problems. The command "within.... {atomno= }" seems to only display exterior holes rather than internal ones. And using command "isosurface interior cavity ___ ", hcp are holes displayed, but cannot find code to display any holes in ccp. For bcc, isosurface interior cavity 0.001 within 5.0 (atomno=11) sasurface 0.04 isosurface interior cavity 0.05 within 5.0 (atomno=11) sasurface 0.04isosurface interior cavity 0.01 within 5.0 (atomno=11) sasurface 0.04 holes shown are quite small, and only shown on the surfaces of the unit cell only. There is no difference observed when "within" parameter omitted isosurface interior canity 0.01 sasurface 0.02 We would welcome any ideas or solutions. All the best Nick -- 3D Organic Animations http://www.chemtube3d.com Tel: +44 (0)151-794-3506 (3500 secretary) |
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