I'm refining a structure of a protein for which the crystallization conditions
include Na/K tartrate. The "Modeling -> Add Other Solvent Molecules -> Add a
new residue" menu in Coot recognized TAR as being tartaric acid, so I used it
to build this molecule. But this is a high-resolution structure wherein I can
discern the actual stereochemistry of this molecule, and it's clearly not the
one that the code is building: the code is building
(2R,3S)-dihydroxybutanedioic acid, i.e. meso-tartaric acid, whereas the true
solvent is the natural, (R,R)-tartaric acid. The label within Coot says it's
building (2S,3S), but I don't think that's actually what's being coded for. I
was able to manually move the incorrect hydroxyl by "Rotate/Translate Zone",
but of course Coot then complains that there's an incorrect chiral volume.
A related peculiarity is that when I invoke the "Add other solvent molecules"
menu, it sometimes labels this compound as TARTARIC ACID, and other times as
"2,3-dihydroxybutanedioc acid". When it labels it as TARTARIC ACID, it knows
what chi angles are available; when it labels it as "2,3-dihydroxybutanedioc
acid", the "Edit Chi Angles" functionality fails.
I'm not an organic chemist, and I don't play one on television. Any thoughts
from the community?
