CCL: Kekule structure asignment - again

 Dear colleagues,
 thanks for the responses so far. Apparently my question was not formulated
clear enough. Having pdb files containing organic molecules but no connectivity 
 records most programs (pymol,sybyl,cactus,babel,weblab viewer ...) are
 able to convert the structure to various formats. However, in most cases,
multiple bonds, aromatic systems etc are not recognized (correctly) just 
 from the
 
 atomic coordinates. Thus a phenyl ring will turn up as cyclohexyl and so on.
 I am sure there is software around which can do this task properly.
 Thanks again,
 Uwe
 (I just tried MOE - no failures up to now, but this isn't exactly freeware.)