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Refining carbohydrates monomers should be as straightforward as refining a protein residue. Coot will look in the dictionary for the 3-letter code for the particular residue type, if it does not find it, Coot will try to search for dictionary files using “-b-D” or “-a-L” extensions.
When refining a group of carbohydrates, the situation needs a bit more explanation. For each residue pair with tandem residue numbers specified in the refinement range selection, Coot checks if these residue types are are furanose or pyranose in the dictionary, and if the are both one or the other, then it tries to see if there are any of the 11 link types (BETA1-4, BETA2-3, ALPHA1-2 and so on) specified in the dictionary. It does this by a distance check of the potentially bonding atoms. If the distance is less than 3.0Å, then a glycosidic bond is made and used in the refinement.
Bonds between protein and carbohydrate and branched carbohydrates can be refined using “Sphere Refinement”.
Instead of using a sphere to make a residue selection, you can specify
the residues directly using refine-residues, for example:
(refine-residues 0 '(("L" 501 "") ("L" 503 "")))
LINK and LINKR cards are not yet used to determine the geometry of the restraints.