Nomenclature issues do not have anything to do with refinement; most
refinement programs including phenix and refmac do not look at them.
Neither does MolProbity.
All it means is that you should swap atom names: OD1 <-> OD2 in case of
ASP, OE1 <- > OE2 for GLU, C[DE]1 <-> C[DE]2 for Tyr and Phe.
Thanks,
Abhinav
JCSG@SSRL, SLAC
Phone: (650) 926-2992
Fax: (650) 926-3292
On 09/15/2011 09:47 AM, 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
