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
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