[phenixbb] following on the anomalous map

Nathaniel Echols nechols at lbl.gov
Mon Aug 25 14:08:26 PDT 2014

On Sun, Aug 24, 2014 at 6:46 AM, CPMAS Chen <cpmasmit at gmail.com> wrote:

> Here is the point I am not clear. If I am using phenix.refine to generate
> LLG map, how do I pick the anomalous group since I have not placed them in
> the model yet?

You can't.  The LLG map only becomes really useful once you have some
anomalous scatterers placed and refined - this is how Phaser substructure
completion works.  If your molecules have no other significant anomalous
scatterers other than the expected Br, the LLG map won't do you much good.

> By the way, when I choose ion_placement and specify Br, the result comes
> with no Br.

Not too surprising, since the code is tuned to look for ions, not part of a
covalent molecule, and halides also tend to bond non-specifically and we
haven't figured out how to deal with that yet.

I want to find whether the Br-containing ligand is seen in my protein which
> I have a high resolution structure available.
> I have data collected at Br wavelength, peak or higher position.
> Phenix.xtriage reported that the anomalous signal is present to about 4A.
> However, both AutoSol or MR-SAD cannot identify the Br position. Simply
> say, AutoSol or MR-SAD can not generate any solution. Well, of course, the
> simple answer would be that there is no such ligand cocrystallized.

The simplest explanation is that you just don't have enough anomalous
signal to determine the substructure, which can be true even if your ligand
is bound.  Running experimental phasing to figure this out is unnecessary
and time-consuming.

Anyway, I am trying to see if the anomalous difference map or LLG(generated
> by phenix.maps, this would be the initial one I assume) can tell me
> anything more useful.
> So, my question on this topic would be what is a better way you guys would
> recommend to identify these Br-ligands? By the way, I did have the native
> datasets for the same protein with ligand.

I think in this case I would start with the simple anomalous difference
map.  If you run phenix.find_peaks_holes (it's in the GUI, of course) and
give anomalous data as input, it can pick out the highest peaks in the
anomalous map.  If the ligand really is bound and the Br site is ordered I
would expect this to be detectable.  Another alternative is to compute an
anomalous isomorphous difference map between a dataset collected at or
above (in eV) the Br peak, and a dataset collected below the peak.  This
will allow you to visualize the wavelength-dependent difference in
anomalous scattering, and it's going to be specific for elements with
absorption edges within that energy range.  But I really don't think this
should be necessary to answer your question.

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