Dear Ed, nice survey page! I have a few comments / questions: - what you mean by "no density", I mean in sigmas? zero? 0.5? multiple apparently alternative locations with 0.7 sigma? or..? Most of the time it is not that the density is zero or negative due to artifacts, but "weak" (I used "" because that needs definition, and probably another survey -:)). Therefore this raises another item for your questionnaire: model each such weak density state with ensemble of alternative conformers (each corresponding to plausible rotamer) and 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). The sum of occupancies may not necessarily add up to 1 because you will still be missing a few conformers with truly no density. - Item #3: I guess if a program lets you to do this during restrained refinement of individual isotropic (or anisotropic) B-factors, then you should submit a bug report. All the flavors of restraints used in individual ADP refinement are essentially similarity restraints that make sure the B-factors of connected atoms are more or less similar. 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. All the best! Pavel. On 3/28/11 7:25 AM, Ed Pozharski wrote:
On Sat, 2011-03-26 at 10:06 +0000, Antony Oliver wrote:
I keenly await the (hopefully) consensus opinion on what we, as crystallographers, should do with residues with poor or absent side-chain density. Antony,
thanks for passing along the information. I won't hold my breath for the consensus though - this is one of the recurring discussions (myself being guilty of repeatedly stoking the fire) that never result in clear conclusion, simply because the choice here has zero effect regarding conclusions drawn from your data. It is simply a question of semantics. To get some idea if there is any indication of consensus, I've set up a survey at google docs
https://spreadsheets.google.com/viewform?hl=en&formkey=dHVNa3VodUtfbVQtZ2pnUFcxQkx6RHc6MQ#gid=0
I'll post the results once it levels off - please don't vote more than once (but feel free to get your lab/family members to have a say).
Cheers,
Ed.