Frank,
PyMOL adds hydrogens based on the hybridization and formal charge of an
atom...if you're not getting the right number of hydrogen, then you probably
need to adjust either the valences of the bonds it participates in, or the
formal charge.
A) To adjust valences:
1) enable "show valences" f
Addis,
Yes, I am aware of this issue and plan to address it in later
versions. Hydrogen adding needs to become residue-aware.
Note that when you are building amino acids, they do start out with
qausi-correct hydrogen names. There is still some ambituity as to which
convention is followed fo
