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 <shabali...@inbox.ru> 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 >
