Pavel,
- what you mean by "no density",
Lack of confidence in placement of the side chain. Everyone would have somewhat different take on it, but the question is more about what to do, not how to decide if the side chain is disordered.
Therefore this raises another item for your questionnaire:
There is "other" option, feel free to use it
refine group occupancy for these atoms (one occupancy per all atoms in question - the occupancy typically will refine to something less than 0.5 or so).
This raises an entirely different question regarding reliability of occupancy refinement in general due to its correlation with the B-factors. Another can of worms.
This trick with smearing out an atom by B-factor may only work for isolated (single) atoms such as waters because they are not bonded to anything through restraints.
Certainly, presence of restraints makes the B-factor increase less steep. I just looked at an instance of a disordered arginine (no density above 1 sigma for any side chain atoms), and B-factors jump from 30 at the backbone to 90 at the tip of the side chain. This would reduce the density level ~5x, which is probably quite sufficient for blending it into the solvent. There could be a bit of a problem in the middle, where B-factors are inflated/deflated, but it does take care of density reduction. Things like atom-specific restraints and modified restraint target may be of some help, but the effect on the final model may be too small to validate the effort. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs