[phenixbb] problem refining Fe-S cluster
Pavel Afonine
pafonine at lbl.gov
Fri Jul 5 08:03:30 PDT 2013
Hi Ed,
it looks like occupancies and B-factors need to be refined and refined
until convergence. Also, if you apply any distance restraints for
clusters (restrain Fe-S distances) make sure these restraints are
correct. I've seen many cases like this and typically refining
occupancy/b-factors and making sure restraints are correct solves the
problem. I've never seen fixing specific parameters help and I can't
understand logic for doing this.
If you get stuck with this you can send me files off list and I'll have
a look.
Pavel
On 7/5/13 7:40 AM, Edward A. Berry wrote:
> I have a problem refining a structure with iron-sulfur clusters. The
> irons refine
> to low B-factors (~25 in this case, while wilson B and B-average are
> around 45
> and the Sg's ligating the irons are ~30). The irons have negative
> difference density
> and there is positive density in the center of the cluster (not on the
> S as it appears;
> the S is actually above the plane of the irons and the positive
> density below).
> (see attached map)
> It's possible that the cluster is lost in some percent of the
> molecules, and I
> could refine occupancy to get rid of the negative density, but I
> suspect this is
> likely to be because the B-factors are too low. I will try manually
> setting B
> for the Fe's and refining without ADP step, but does anyone have a
> better suggestion?
> This was refined for one macrocycle with
>
> strategy = *individual_sites individual_sites_real_space rigid_body \
> *individual_adp group_adp tls *occupancies group_anomalous
> thanks,
> eab
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