James, this may be one of those physics-vs-math arguments again. Surely the occupancy can be used to account for everything, but it makes it a fudge factor. I'd say the right way is to use the adjusted scattering factors first (after all, that is something we do know about the experiment), and if there is still a residual density then one cannot distinguish between radiation damage and partial Se-Met incorporation and has to resort to occupancy, realizing that it's meaning is somewhat unclear.
Cheers, Ed. On Tue, 2011-11-01 at 08:42 -0700, James Holton wrote: > Collecting "close to the edge" where the cross section of Se is higher > does indeed increase the absorbed dose per scattered photon (Muray et > al. JSR, 2005), but wavelength has absolutely no impact on the relative > "rate" of Se-C bond breakage (Holton JSR 2007). The number of Se-C > bonds broken is proportional to the total amount of energy absorbed, not > the atom type that initially absorbed it. In fact, most of the Se-C > bonds will break long before even a few percent of the Se atoms have > been hit by a photon. > > But yes, rad dam could be a reason for the negative peaks. Formally, > this is not a change in occupancy, since the Se atoms does not actually > leave the crystal or otherwise vanish from the universe, it just gets a > very high B factor, and the centroid of its position probably moves away > from the carbon atom. It is hard to say. This is why lowering the > occupancy is as good a model as any. > > Negative peaks can also come from scaling errors. Remember, a Se atom > with B=24 is 10 e-/A^3 tall, whereas a C with the same B factor is only > 1.3 e/A^3 tall. So, if you have a ~3% error in the scale factor, it > will show up on the Se atoms first, and unless you have every single > atom modeled, the scale factor of Fcalc will tend to be a bit high. > > Practically speaking, occupancy refinement is a perfectly good way to > model all of the above phenomena. Yes, changing the f' value is the > "right" way to do it, but no doubt you've got other things going on as > well, and the electron density cannot distinguish between them. For > example, if you compare the calculated electron density for an Se atom > with B=24 and f' = -8 vs that of an Se with B=25.54 and occ=0.754, the > curves are less than 0.1% different. This is because when B>~10, all > the details of the atomic form factor are blurred out by the much wider > B-factor Gaussian. It doesn't hurt to model the atoms form factors > properly, but in almost all cases of MX, some other source of error is > more important. > > -James Holton > MAD Scientist > > > On 11/1/2011 6:55 AM, Ed Pozharski wrote: > > On Mon, 2011-10-31 at 15:57 +0000, Ivan Shabalin wrote: > >> As a result, red peeks around Se are significantly lower, Se B-factors are > >> a bit smaller (like 25.6 and 23.1), and Rf is lowered by a bit more than > >> 0.1% with the same input files. > > Hope others will comment to clarify my confusion: > > > > It seems that the potential effect of correcting the structure factor > > data depends strongly on how close to the edge you are: > > > > The reduction of the overall scattering factor has a steep wavelength > > dependence. For example, the Se atom has 34 electrons, so that should > > be a rough estimate of its scattering factor in the absence of > > absorption. At the very edge, f'~-8 electrons, which seems equivalent > > to the ~80% occupancy, or the difference density peak on par with that > > of a water molecule. I guess it's also true that close to the edge you > > will have more damage, thus the negative density. > > > > Other words, is it possible that Ian (and others) do not see a > > significant effect from correcting the scattering factors because they > > do not collect close to the edge, while Ivan might have done exactly > > that? > > > > Cheers, > > > > Ed. > > > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
