[phenixbb] Refining anomalous groups

Felix Frolow mbfrolow at post.tau.ac.il
Sat Jan 12 00:05:38 PST 2013

Hi Nath,
Happy 2013!
Is it possible to use anomalous automatism also under GUI?
Will be the event of refinement of anomalous dispersion parameters f' and f" recorded in PDB file?
Dr Felix Frolow   
Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfrolow at post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Jan 9, 2013, at 22:38 , Nathaniel Echols <NEchols at lbl.gov> wrote:

> On Wed, Jan 9, 2013 at 12:26 PM, Brennan Bonnet
> <Brennan.Bonnet at lightsource.ca> wrote:
>> I hope everyone had relaxing holidays to begin the new year.  I am back to work trying to refine anomalous groups using phenix.refine.
>> I have managed to merge my files so that my exptl_fobs_phases_flags_1_with_hl_anom.mtz now contains F(+), SIGF(+), F(-), SIGF(-).
>> Now I have a new problem which was not occurring before the break.  Usually I check the box for "Anomalous groups", then select "Modify selections for: Anomalous groups" which brings up a screen for atom selection and definition of f' and f''.  In the past, clicking on the View/pick button launches Coot for selection of the atoms.  Sadly, now clicking on the View/pick doesn't launch Coot and instead crashes Phenix.
> What OS (including version) are you using, which Phenix installer did
> you use (including the exact package name), and could you please send
> me any error messages printed to the console?  The built-in graphics
> is spectacularly difficult to get working on some Linux systems, for
> reasons I still don't understand.  However, I don't think those
> buttons ever launched Coot - maybe something that looks superficially
> similar, perhaps, but it's obviously stopped working on your computer.
> I do have a suggestion for working around this, but it's a pain to
> use: a few weeks ago I added an option to set up the anomalous groups
> automatically.  You have to choose the "Edit parameters and run"
> option when starting phenix.refine, then look for this parameter
> (heavily condensed):
> refinement {
>  group_anomalous {
>    find_automatically = False
>  }
> }
> Change that to True, and every atom heavier than P will be treated as
> a separate anomalous group.  (This is not necessarily the optimal way
> to do it, which is why it's hidden right now, but it worked well for
> the tests I've done so far.)
> -Nat
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