Hello everyone,
Perhaps this is a newbie question, so I apologize.
After much work and a lot of thanks to the ccp4 bulletin board I just tried to
submit my first structure to the pdb database. It is a membrane protein and
therefore has some detergent molecules bound to it. I received an email back
from the lady who authorizes the structures indicating that the stereochemistry
of many of my beta octylgluside molecules are incorrect. Needless to say I am
not a chemist, and therefore the subtleties of sugar ring enantiomers were not
immediately apparent to me, however I now understand how the hydroxyls must be
pointing for the molecule to satisfy the BOG criteria. My question is that
shouldn't the .cif file, in this case libcheck_BOG.cif (COOT generated when I
get the monomer from the coot library) contain these enantiomeric restrictions?
Even if I change the carbons of the beta glucoside manually, shouldn't the
correct stereochemistry be restrained during the refinement? Thanks so much for
any help with this complicated question.
Drew
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