[phenixbb] Iron (FE2) metalloprotein

Nathaniel Echols nechols at lbl.gov
Mon Jun 23 21:45:25 PDT 2014

On Mon, Jun 23, 2014 at 9:35 PM, Egor Tchesnokov <
etchesnokov at chemistry.otago.ac.nz> wrote:

>  Active site contains iron (FE2) coordinated by three histidines.
> After Phaser the active site does not contain un-explained green density.
> After Refinement blobs of various shapes appear in the vicinity  and upto
> 3-4A of active site iron.
> Refinement is done using occupancy and anomalous of iron options.
> Buffers do not contain molecules that could fit in those blobs.

Phaser resets all heteroatoms to zero occupancy unless you specifically
request otherwise, and I don't think refinement will magically take care of
that.  If you're using the GUI, click the button labeled "Modify start
model" in the middle configuration tab, choose occupancies, and enter 1 for
the new occupancy.  (The occupancy refinement will still take place.)  Or
you can just do this manually in PDBtools or the PDB editor.

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