*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Since the combined effects of an inaccurate f' value, partial Se
incorporation and radiation damage are difficult to predict, and the
latter may be different for different Se atoms in the same structure, it
is always interesting to refine the selenium occupancies (either
independently or constrained to be equal); this can significantly reduce
Rfree and always gives occupancies less than unity. A minor complication
is that (at present) it requires refining with SHELX; you also need to
include a DISP instruction to set f' and f" to suitable values for the
Se and possibly other atoms.
George
Peter Adrian Meyer wrote:
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Ethan Merritt wrote:
I was asked off-list if the failure to replace scattering
factors in atomsf.lib could also explain negative electron
density at Se sites in maps made for SeMet proteins.
The short answer is "yes, but..."
The longer answer continues...
<long answer removed>
Following this logic (for general anomalous stuff, not necessarily Se),
shouldn't this be done for all atoms, not just the anomalous sites?
Unfortunately, I could argue this both ways (which is a sure sign I'm
confused):
For - numerous small changes in f' from non-anomalous atoms will add up
for larger structures; and even for smaller structures it's probably
better if the model is as accurate a description as possible of the data
(and would probably improve the statistics).
Against - probably no way to measure f' of the non-anomalous atoms (unless
there's some way to de-convolute the fluroescence scan, which is dominated
by the anomalous atoms), so you'd have to use calculated values; f' is not
resolution-dependent, so errors here can be absorbed by the scale factor
(however, this is somewhat of a fudge factor, seeing as it's unlikely that
the variation in f' for all atom types is uniform).
Is this something that people generally worry about during refinement?
Pete
Pete Meyer
Fu Lab
BMCB grad student
Cornell University
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
