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
Example steps to reproduce
zoom resi 12
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.
Esben Jannik Bjerrum