It's up to you to decide how you want to handle this. You have a few options.
You can remove unwanted alternate conformations, for example:
remove not alt ''+'A'
then run your script.
Or you can specify PyMOL only add hydrogens to a certain set of conformations:
# only h_add to alt conformations labeled 'C'
h_add 1zw9 and alt 'C'
To only add hydrogens to default or 'A' conformers do the following:
h_add 1zw9 and alt ''+'A'
On Thu, Apr 18, 2013 at 3:59 AM, Esben Jannik Bjerrum
> 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
> 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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