pafonine at lbl.gov
Mon Mar 28 08:20:11 PDT 2011
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!
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
> 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
> 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).
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