[phenixbb] heavy atoms

Pavel Afonine pafonine at lbl.gov
Wed Jun 1 05:53:02 PDT 2011

Hi Tiantian,

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

2) Try:
  - refine individual anisotropic ADP for these atoms (and isotropic for 
the rest);
  - occupancy;
  - define charge in input PDB file;
  - if it is anomalous scatterer use and refine f' and f''.

Hope this helps.

> Hi,
> 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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