[phenixbb] Refining anomalous groups

Nathaniel Echols nechols at lbl.gov
Sat Jan 12 09:58:39 PST 2013

On Sat, Jan 12, 2013 at 12:05 AM, Felix Frolow <mbfrolow at post.tau.ac.il> wrote:
> Is it possible to use anomalous automatism also under GUI?

Yes, in the current nightly build, do the following:

1. From the phenix.refine GUI, open Settings->Advanced->Group
anomalous refinement
2. Change the "User level" menu to "Developer"
3. Activate the checkbox labeled "Find automatically"

There's probably no reason why it needs to be this hidden - it seems
very safe so far, but until we've had more chances to test it we
prefer to minimize the number of features that can potentially break.

> Will be the event of refinement of anomalous dispersion parameters f' and f"
> recorded in PDB file?

I am not sure whether phenix.refine includes anything in the headers -
it appears not.  Unfortunately there is no way to incorporate these
into the coordinate records themselves either.  However, once we have
full support for mmCIF (Richard Gildea is working on this, and it is
very close), that will indeed support both writing out and reading in
the refined anomalous scattering.  Will discuss this with Richard and


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