Here is another set of relavant papers and instructive pictures: 1) CCP4 Newsletter http://www.ccp4.ac.uk/newsletters/newsletter42/content.html On the Fourier series truncation peaks at subatomic resolution Anne Bochow, Alexandre Urzhumtsev
2) Some Facts About Maps (pages 30, 32, 33): http://www.phenix-online.org/presentations/latest/pavel_maps.pdf 3) Page 267 Figure 4: On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps P. V. Afonine, V. Y. Lunin, N. Muzet and A. Urzhumtsev Acta Cryst. (2004). D60, 260-274 4) Central Ligand in the FeMo-Cofactor Nitrogenase MoFe-Protein at 1.16 Å Resolution: A. Oliver Einsle, et al. Science, 1696 (2002) 297 5) Numerous pictures of density as function of distance from atom center for various B-factors: Acta Cryst. (2004). A60, 19-32 On a fast calculation of structure factors at a subatomic resolution P. V. Afonine and A. Urzhumtsev Pavel. On Fri, Dec 24, 2010 at 1:31 PM, Bernhard Rupp (Hofkristallrat a.D.) < [email protected]> wrote: > In reference to the low and high B atoms in a map and the ripples, one can > actually calculate something of educational value using my web applets > (with > all the caveats imposed by simplicity of the 1-d case). Here is how: > Go to > http://www.ruppweb.org/new_comp/structure_factors.htm > and set the B-value of the C atom to 100 (yes it takes integer 100 in > contrast to instructions) and the B-value of the O atom to 2. Leave the > default for the rest and execute (you can pick a name for the SF file if > you > like). > then goto > http://www.ruppweb.org/new_comp/fourier_maps.htm > set the grid to 100 and optionally enter the file name you used before > and execute > > Look at the resulting map and the peak shapes. The relative scale, > broadening, and ripples all show up as discussed. > > Merry Christmas, BR > > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Ian > Tickle > Sent: Friday, December 24, 2010 4:26 AM > To: [email protected] > Subject: Re: [ccp4bb] Resolution and distance accuracies > > 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 > <[email protected]> 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 > >> > > >
