Privateer just requires a model and a set of reflections (including sigmas) to work (1). The model will be scanned for known cyclic carbohydrates (some popular Nitrogen-substituted compounds are also supported) and then the structure factor and map coefficient calculations will begin. Sugars will be omitted from phase calculation, effectively producing omit mFo-DFc map coefficients.
Once Privateer has calculated model and experimental electron densities, a correlation analysis is performed within the boundaries of a mask calculated around the studied sugar. This mask can be adjusted by tweaking its radius, as shown below. Then, a conformational (using the Cremer-Pople algorithm) and stereochemical analysis will follow.
It is possible to analyse a single sugar (supported or not) by typing its three-letter code in (2). The sugar model must follow the standard naming scheme, with C1-C5 plus O5 in the ring (C2-C6 plus O6 for ketoses).
It is possible to change the radius for the mask that is used for the correlation analysis (3). A typical value would be between 1.5 to 2.5 Angstroems, with smaller values being more forgiving with modelling errors than higher ones.
Weak density gradients
Sometimes there is just partial density for a sugar that is known to be there (e.g. in a High-Mannose glycosylation tree), and it is the crystallographer's decision whether to model it or not. However, atempting to refine a model with such data without the appropriate restraints - torsion restraints can help in this case - will nearly always result in distortion.
Wrong linkage distance specification
Forcing refinement software to restrain a link to a wrong distance will make it fit the model with an offset equal to the deviation from the correct value. This can result just in an increased total puckering amplitude (Q) value if the deviation is not too high, or a complete conformational change for higher values.
Mistaken anomer or handedness
Trying to fit an alpha anomer into density that supports the beta anomer instead will result on a flat ring or a conformational change.