Janocchio does not generate three dimensional structure files itself. It requires structures to be supplied as mol, sd or xyz files. How these are created is up to the user, but clearly there will be a correlation between quality of the input and the output. For small relatively rigid structures, a simple energy minimization may be sufficient to generate a structure, but more typically a conformational search would be performed. To do conformational analysis in Janocchio, either by scanning through possible conformers, or by using NAMFIS, it is often useful to cluster structures so as to reduce the number of input conformers to the minimum required to be representative. It is also advised to overlay multi conformer files over a common molecular core if possible: this makes comparisons between conformer frames much simpler, and makes the populated conformer overlay much more useful.