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.
