   Antialiasing Problem
  I have drawn a molecular structure. i show the bonds with cylinders and atoms with spheres. the problem is that when i perform antialiasing then some part of sphere is hide by the cylinder and cylinder comes on the top. so visualization is not looking good. can any one help me?   
  Some screenshots would be good, but to me it sounds like your zbuffering is out of whack, dont know how antialiasing would affect that, but thats the best i can do without a screenshothope that helps-Dan   