[phenixbb] Iron (FE2) metalloprotein

Nathaniel Echols nechols at lbl.gov
Tue Jun 24 08:21:58 PDT 2014

On Tue, Jun 24, 2014 at 1:11 AM, Egor Tchesnokov <
etchesnokov at chemistry.otago.ac.nz> wrote:

>  Thank you for the comment.
> The model I use for Phaser is coming from Sculptor, so it does not have
> heteroatoms.
> I introduce heteroatom (Fe) only after Phaser. I use Phaser-EP to find it,
> eventhough it is obvious from the density. Then I merge Fe and Phaser.pdb
> in Coot after which I feed it to ReadySet. So the pdb that I give to Refine
> either have Fe with occupancy of 1, <1 or >1 (I tried both). I use PDB
> editor to add charge, but the outcome is still the same. After refinement
> Fe occupancy is either 1 or very close.

My apologies, I misinterpreted your message.  Is this just a case of "name
that blob?"  If so, I suggest posting images of the density around the iron
to the list (and probably ccp4bb as well) asking for suggestions.  It's
very likely that someone will have encountered similar density before.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20140624/e57dcc45/attachment.htm>

More information about the phenixbb mailing list