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
