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...
Best!
João
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