The OMIT map is calculated like a normal map, but with a certain region of the structure being omitted when calculating Fcalc.
A usual electron density map in macromolecular crystallography is calculated from both experimental (Fobs) and calculated (Fcalc) structure factors. Fcalc (structure factors calculated from the model) are necessary to get approximate phases. This causes model bias - the obtained electron density is skewed toward the model and might seem to confirm a model that's not truely supported by the experimental data. The idea of the OMIT map is that you exclude a certain region when calculating structure factors (this region can be modelled as bulk solvent instead – a flat electron density). If the region is relatively small, it won't degrade the overall map quality too much, but it will remove the bias in this particular region. It's a trick to validate if a ligand is really there. Marcin
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