To get an idea about this signal:noise issue, I wonder what the B factor of bulk solvent would be, if it is possible to think in such terms, i.e., fill the bulk solvent with dummy waters and let the B's do what they will. I wonder whether anyone has tried explicitly modelling the whole unit cell this way, and what the effects were? I imagine it might be possible at ultra-high resolution. In other words, I am wondering whether the electron density for a 100-B-factor atom is significantly different from bulk solvent.
Jacob On Fri, Dec 24, 2010 at 6:26 AM, Ian Tickle <ianj...@gmail.com> wrote: > I have a program which computes the atomic electron density profile > (attached) as you would see it in a map, using accurate scattering > factors and taking the resolution limit into account. I wouldn't call > the profile for a C atom with B=100 at 2.5 Ang resolution 'flat', > maybe 'flatter'. 'Flat' would imply that it's lost in the noise of > other atoms with B=100. > > My point is that it's relative. Since my average B is 85 Ang.^2, an > individual B of 100 or even 120 doesn't seem out of the ordinary at > all. If the average B were 10 then I would agree that anything over > say 50 would appear flat and insignificant. > > The reason I think is simply that atoms with low B factor have series > termination ripples around them which can swamp the density of other > atoms with high B factor (for example the ripples from a B=10 C atom > are half the height of the peak of a B=150 atom). So the net 'noise' > level in a map with low average B is much higher than in one with high > average B, so that any atoms with high individual B just get lost in > the noise. > > Cheers > > -- Ian > > On Thu, Dec 23, 2010 at 8:05 PM, Ronald E Stenkamp > <stenk...@u.washington.edu> wrote: >> Something related to the results in the 1984 paper, but never published, is >> that the calculated electron density for an atom with a B of 100 >> Angstroms**2 is so flat that you wonder how those atoms can be seen in >> electron density maps. >> >> Ron >> >> On Thu, 23 Dec 2010, Bernhard Rupp (Hofkristallrat a.D.) wrote: >> >>>> can anyone point me to a more exact theory of distance accuracy compared >>> >>> to >>>> >>>> optical resolution, preferably one that would apply to microscopy as >>>> well. >>> >>> Stenkamp RE, & Jensen LH (1984) Resolution revisited: limit of detail in >>> electron density maps. Acta Crystallogr. A40(3), 251-254. >>> >>> MX, BR >>> >> > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *******************************************
