Hey Jason!

Thanks for the reply, no problem at all with the delay :)

I got my hands around the code and I *think* I got it to add hydrogens to a protein (including checking that random effect).

My only question is, how PyMol determines which atoms lack hydrogens. I checked the hetatm.py and protein.py files and they seems to compare the structure with a pre-defined database of bonds for each residue. However, this works for proteins only right?

How does it work for methane? How does it recognize that is lacks 4 atoms? If you can point me to the file where that part is described, that would be amazing! I've lost two weeks trying to figure it out already and I can't...