[phenixbb] heavy atoms
pafonine at lbl.gov
Wed Jun 1 05:53:02 PDT 2011
it is pretty popular question. Here is copy-paste from my previous reply
to similar question:
a few things to consider:
1) Fourier truncation ripples:
- CCP4 Newsletter
On the Fourier series truncation peaks at subatomic resolution
Anne Bochow, Alexandre Urzhumtsev
- Pages 52-55 here:
- Oliver Einsle, et al. Science, 1696 (2002) 297
- Page 267 Figure 4:
Acta Cryst. (2004). D60, 260-274
- refine individual anisotropic ADP for these atoms (and isotropic for
- define charge in input PDB file;
- if it is anomalous scatterer use and refine f' and f''.
Hope this helps.
> I am dealing with a complex structure which the ligand contains a atom
> Iodine, I guess it's because Iodine is heavy atom,
> the electron density of Iodine turns red after 5 cycles refinement.
> Anybody coped with similar issue?
> How to let phenix know that the Iodine atom is part of the ligand?
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