Hi, personally I didn't find that changing scattering factors for Se,
Br, I etc made a big difference to the maps. The more likely
explanation seems to be site occupancy disorder due to
radiation-induced breaking of covalent bonds, in which case you need
to refine the occupancy. But maybe it's a bit of both. I don't see
any harm in specifying the correct value of f' (as long as obviously
it is the correct value!).
Cheers
-- Ian
On Mon, Oct 31, 2011 at 3:57 PM, Ivan Shabalin <[log in to unmask]> wrote:
> Dear Refmac users,
>
> I noticed that if I refine a structure containing SeMet, then Se atoms usually have big negative (red) peeks of difference map and high B-factors. As I understand from the diffraction theory and from some discussions at CCP4bb, that may result because in REFMAC the atomic scattering factors are internally coded for copper radiation (CuKa).
> I tried to use keyword "anomalous wavelength 0.9683" and found that with this keyword I had different values of coefficient c for Se, Mn, and P as shown in REFMAC log-file:
>
> loop_
> _atom_type_symbol
> _atom_type_scat_Cromer_Mann_a1
> _atom_type_scat_Cromer_Mann_b1
> _atom_type_scat_Cromer_Mann_a2
> _atom_type_scat_Cromer_Mann_b2
> _atom_type_scat_Cromer_Mann_a3
> _atom_type_scat_Cromer_Mann_b3
> _atom_type_scat_Cromer_Mann_a4
> _atom_type_scat_Cromer_Mann_b4
> _atom_type_scat_Cromer_Mann_c
>
> N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290
> C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156
> H 0.4930 10.5109 0.3229 26.1257 0.1402 3.1424 0.0408 57.7997 0.0030
> O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508
> SE 17.0006 2.4098 5.8196 0.2726 3.9731 15.2372 4.3543 43.8163 -1.0329
> MN 11.2819 5.3409 7.3573 0.3432 3.0193 17.8674 2.2441 83.7543 1.3834
> P 6.4345 1.9067 4.1791 27.1570 1.7800 0.5260 1.4908 68.1645 1.2650
>
> 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.
>
> That looks pretty good. Still, I want to ask your opinion on the following:
>
> 1) Is it proper way to specify atomic scattering factors? I found this keyword under REFMAC documentation topic "Simultaneous SAD experimental phasing and refinement" and Im not sure if I change something else when I specify the keyword. I dont have separate F+, F- and corresponding SIGF+, SIGF- in my mtz, so SAD experimental phasing should not go.
> 2) Do you think it is safe to specify this keyword for every structure under refinement? Can it have some drawbacks (except wrong wavelength)?
> As I understand, the theoretical Cromer_Mann curve can be different from experimental, but still it is better than not to change scattering factor at all.
>
> Thank you very much!!
>
> With best regards,
> Ivan Shabalin, Ph.D.
> Research Associate, University of Virginia
> 4-224 Jordan Hall, 1340 Jefferson Park Ave.
> Charlottesville, VA 22908
>
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