Google is your friend: http://www.biop.ox.ac.uk/coot/doc/coot/Fix-Nomenclature-Errors.html
Yes, that dialog freaked me out at first too, but from what I understand it just fixes ambiguities (e.g Phe/Tyr flips and such). On Thu, 2011-09-15 at 09:47 -0700, Engin Özkan wrote: > Dear coot users and developers, > > We are using coot 0.7-pre-1 (rev 3633) in the lab on linux and Mac > machines, and have observed something odd that we did not see before. > Most (all?) pdb files when opened give a (harmless) warning that says > "Molecule x has nomenclature errors. Correct them?" The residues > mentioned are Phe's, Tyr's, and Asp's. I don't think there was an update > to these residues in the latest dictionary. Before I go into more > detail, is anybody else seeing this, and should we just install a newer > nightly? > > I should note that these models have been refined by Phenix versions 1.6 > and 1.7, and molprobity thinks they are perfectly fine. There are no > DNA/RNA bases, and odd ligands, except sugars in them. > > Best, > Engin -- Coot verendus est
