(* Si(CH3)4 computation; coordinates and radii from Sime40D7.exe, 12.02.2012 *)
t={{0.00000,0.00000,0.00000,0.59670},{1.93276,0.00000,0.00000,1.33606},{3.54930,0.00000,0.00000,0.28048},{4.02033,-1.33227,0.00000,1.13260},{4.02033,0.66614,1.15378,1.13260},{4.02033,0.66614,-1.15378,1.13260},{-0.64425,1.82222,0.00000,1.33606},{-1.18310,3.34631,0.00000,0.28048},{-2.59619,3.34631,0.00000,1.13260},{-0.71207,4.01245,1.15378,1.13260},{-0.71207,4.01245,-1.15378,1.13260},{-0.64425,-0.91111,1.57809,1.33606},{-1.18310,-1.67316,2.89799,0.28048},{-2.59619,-1.67316,2.89799,1.13260},{-0.71207,-3.00543,2.89799,1.13260},{-0.71207,-1.00702,4.05177,1.13260},{-0.64425,-0.91111,-1.57809,1.33606},{-1.18310,-1.67316,-2.89799,0.28048},{-2.59619,-1.67316,-2.89799,1.13260},{-0.71207,-1.00702,-4.05177,1.13260},{-0.71207,-3.00543,-2.89799,1.13260}};
u={{0.00000,0.00000,0.00000},{3.54930,0.00000,0.00000},{4.20661,-1.85915,0.00000},{4.20661,0.92957,1.61007},{4.20661,0.92957,-1.61007},{-1.18310,3.34631,0.00000},{-3.15502,3.34631,0.00000},{-0.52579,4.27589,1.61007},{-0.52579,4.27589,-1.61007},{-1.18310,-1.67316,2.89799},{-3.15502,-1.67316,2.89799},{-0.52579,-3.53230,2.89799},{-0.52579,-0.74358,4.50806},{-1.18310,-1.67316,-2.89799},{-3.15502,-1.67316,-2.89799},{-0.52579,-0.74358,-4.50806},{-0.52579,-3.53230,-2.89799}};

x=Table[t[[i,1]],{i,1,21}];
y=Table[t[[i,2]],{i,1,21}];
z=Table[t[[i,3]],{i,1,21}];
r=Table[t[[i,4]],{i,1,21}];

h=Table[u[[i,1]],{i,1,17}];
k=Table[u[[i,2]],{i,1,17}];
l=Table[u[[i,3]],{i,1,17}];

(* xy plane *)
Clear[plot2,plot2a,plot2b];
plot2=Table[Graphics[{Circle[{t[[i,1]],t[[i,2]]},t[[i,4]]]}],{i,1,21}];
plot2a=Table[Graphics[{Disk[{h[[i]],k[[i]]},0.08]}],{i,1,17}];
plot2b=Graphics[{Thickness[0.006],Line[{{h[[2]],k[[2]]},{h[[1]],k[[1]]}}],Line[{{h[[1]],k[[1]]},{h[[6]],k[[6]]}}],Line[{{h[[1]],k[[1]]},{h[[10]],k[[10]]}}],Line[{{h[[1]],k[[1]]},{h[[14]],k[[14]]}}],Line[{{h[[2]],k[[2]]},{h[[3]],k[[3]]}}],Line[{{h[[2]],k[[2]]},{h[[4]],k[[4]]}}],Line[{{h[[2]],k[[2]]},{h[[5]],k[[5]]}}],Line[{{h[[6]],k[[6]]},{h[[7]],k[[7]]}}],Line[{{h[[6]],k[[6]]},{h[[8]],k[[8]]}}],Line[{{h[[6]],k[[6]]},{h[[9]],k[[9]]}}],Line[{{h[[10]],k[[10]]},{h[[11]],k[[11]]}}],Line[{{h[[10]],k[[10]]},{h[[12]],k[[12]]}}],Line[{{h[[10]],k[[10]]},{h[[13]],k[[13]]}}],Line[{{h[[14]],k[[14]]},{h[[15]],k[[15]]}}],Line[{{h[[14]],k[[14]]},{h[[16]],k[[16]]}}],Line[{{h[[14]],k[[14]]},{h[[17]],k[[17]]}}] } ];

Show[plot2,plot2a,plot2b,{AspectRatio -> Automatic,Axes -> True,GridLines -> Automatic, PlotRange -> {{-5.5,5.5},{-5.5,5.5}}, Frame -> True}]

plot3=Table[Graphics3D[{Opacity[0.6],Sphere[{t[[i,1]],t[[i,2]],t[[i,3]]},r[[i]]]}],{i,1,21}];
plot3a=Table[Graphics3D[{Darker[Red,1.0],Sphere[{u[[i,1]],u[[i,2]],u[[i,3]]},0.15]}],{i,1,17}];
plot3b=Graphics3D[{ Tube [{{h[[2]],k[[2]],l[[2]]},{h[[1]],k[[1]],l[[1]]}},0.08], Tube [{{h[[1]],k[[1]],l[[1]]},{h[[6]],k[[6]],l[[6]]}},0.08], Tube [{{h[[1]],k[[1]],l[[1]]},{h[[10]],k[[10]],l[[10]]}},0.08], Tube [{{h[[1]],k[[1]],l[[1]]},{h[[14]],k[[14]],l[[14]]}},0.08], Tube [{{h[[2]],k[[2]],l[[2]]},{h[[3]],k[[3]],l[[3]]}},0.08], Tube [{{h[[2]],k[[2]],l[[2]]},{h[[4]],k[[4]],l[[4]]}},0.08], Tube [{{h[[2]],k[[2]],l[[2]]},{h[[5]],k[[5]],l[[5]]}},0.08], Tube [{{h[[6]],k[[6]],l[[6]]},{h[[7]],k[[7]],l[[7]]}},0.08], 
Tube [{{h[[6]],k[[6]],l[[6]]},{h[[8]],k[[8]],l[[8]]}},0.08], 
Tube [{{h[[6]],k[[6]],l[[6]]},{h[[9]],k[[9]],l[[9]]}},0.08], Tube [{{h[[10]],k[[10]],l[[10]]},{h[[11]],k[[11]],l[[11]]}},0.08], Tube [{{h[[10]],k[[10]],l[[10]]},{h[[12]],k[[12]],l[[12]]}},0.08], Tube [{{h[[10]],k[[10]],l[[10]]},{h[[13]],k[[13]],l[[13]]}},0.08], Tube [{{h[[14]],k[[14]],l[[14]]},{h[[15]],k[[15]],l[[15]]}},0.08], Tube [{{h[[14]],k[[14]],l[[14]]},{h[[16]],k[[16]],l[[16]]}},0.08], Tube [{{h[[14]],k[[14]],l[[14]]},{h[[17]],k[[17]],l[[17]]}},0.08] } ];

Show[plot3,plot3a,plot3b,{AspectRatio->Automatic,SphericalRegion->True}]