Hi Pymol Users
    I have a problem with wrong atom assignment, and subsequently wrong addition of hydrogens, if theres alternate conformations present. I hope anyone else has experience with this or suggestions for troubleshooting.
    I have developed some scripts that downloads pdb-files from a list, add hydrogens to them, and otherwise prepares them for further usage. However, if theres alternate conformations present, the atoms on the backbone gets a wrong charge assignemt or something, breaking the subsequent addition of hydrogens. It seems to happen at PDB load time.

Example steps to reproduce
fetch 1zw9
zoom resi 12
h_add 1zw9

the hydrogen on the nitrogen in the backbone peptide bond doesn't make a planer configuration, and if I save the object, the oxygen is assigned a -1 charge. This makes troubles in my subsequent workflow.

I've tried to delete the alternate conformations inside PyMOL before adding hydrogens, but that doesnt fix the problem. I can fix the problem by removing the alternate conformations from the PDB file before I load it into pymol, but I would rather fix it inside pymol in my scripts.

Best Regards
Esben Jannik Bjerrum