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If atom sizes are the same, then all pictures will have different width.
So if I scale them to have the same width, then atom sizes will become different.

That is the problem, that vector graphic doesn't have its original "size". It is always scaled to what a user or a program define.

Thanks for ...

If I use set width, I still get different size on the text on the vector graphs, because all pictures have different size with 12cm width (see attachment).

Hi,
I have several vector-graphs with molecule structures (carbon atoms connected by lines: H2C=CH-CH3). They all have different length/height/aspect ratio.
I have them in .emf format.
When I put them in the LyX document and make a pdf, all of them are scaled differently.
Bigger molecules have atoms ...