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Thanks everybody for the profound answers! As a summary, I can list the following reasons for the negative density defects at Se atoms: 1) the default scattering factors for Se are incorrect for wavelengths that are not close to CuKA, even though it may be not the major source of errors. Also, it is dependent on the wavelength - closer to the peek of Se>> more impact. This factor we can correct for sure. 2) the fractional incorporation of Se is often less than 100%. And it may be difficult to estimate. 3) radiation-induced breaking of covalent bonds, which is independent of the wavelength (!!!) 4) scaling errors. "So, if you have a ~3% error in the scale factor, it will show up on the Se atoms first, and unless you have every single atom modeled, the scale factor of Fcalc will tend to be a bit high" - James Holton 5) both regular methionine and selenomethionine have somewhat disordered sidechain conformations, and that can result in bigger Se (S) B-factors. There is no harm in specifying the correct value of f' (I did it through the wavelength specification), It may help a little and obviously is correct. Also, one can model partial occupancy for Se atom. But one should understand that this can be a fudge factor. As general conclusion, one can recommend to decrease occupancy of Se if the red peek is very big. I was intrigued by James Holton saying that "when B>~10, all the details of the atomic form factor are blurred out by the much wider B-factor Gaussian" Does that mean, that with Bf>10 we cannot distinguish Mg and water by electron density peak profile? Even if oxygen in water has twice as much bigger radius than Mg2+? I have one more question about modelling ions and im going to ask it in a separate post. Thanks a lot!! With best regards, Ivan Shabalin