How to draw many structures

A skeleton file stores the general layout of a previously made drawing. This layout can be applied to your new structure. The closer the new structure resembles the one from which the skeleton files was made, the better the resulting drawing, and the less work you will have 'beautifying' the result. So, in order to draw many (related) structures, it is good to have a good skeleton file.

So, if you want to draw the structure of several related species, it is better to first create a skeleton file for this group than to use a general skeleton (e.g. that from E. coli for all drawings. You can do this by making a structure drawing for one representative of the group using a general skeleton file (or even without a skeleton).

From this drawing you can create a new skeleton, which will be better fit for the group, and use this to create drawings for all the other drawings in the group.