[phenixbb] Merging reflections

[mohamed noor]

Tom, just out of curiosity, do I need to delete the ligand or can I just
set the occupancy to 0? AFAIK, Phaser does the latter automatically anyway.


On Mon, Jun 1, 2015 at 10:19 PM, Terwilliger, Thomas Charles <
terwilliger at lanl.gov> wrote:

> Hi Mohamed,
>
> If you have good data to 3 A and a search model, go ahead and use MR to
> solve the structure.  Just delete the ligand from the search model and you
> won't have model bias and you can see if the ligand is there.
>
> You might use the anomalous signal to check your solution by calculating
> an anomalous difference Fourier after you have obtained an MR solution.  It
> should have a peak at the position of your Mo atom, perhaps visible even if
> the anomalous data are pretty weak.
>
> The signal in your anomalous data may be much smaller than the errors in
> measurement in some of your datasets.  In that case you wouldn't be able to
> see it.
>
> All the best,
> Tom T
>
>
> On Jun 1, 2015, at 3:09 PM, mohamed noor wrote:
>
> > Dear all
> >
> > I have a few native datasets, one anomalous dataset with signal up to 10
> A and two other datasets (also collected at the phasing wavelength but no
> anomalous signal seems to be present) and a sulfur SAD dataset with signal
> to about 7 A. All the datasets have a resolution of about 2-3 A and
> processed with xia2/XDS.
> >
> > I couldn't do fluorescence scan as the detector couldn't detect at such
> a high energy (20 keV).
> >
> > A few questions:
> >
> > 1. Why is there at least some signal from one dataset but not others?
> The signal should come from a covalently bound ligand, molybdopterin to be
> precise.
> >
> > 2. Since I(+) should not be equal to I(-) when there is anomalous
> signal, should I just merge the native dataset together with those
> collected at phasing wavelength that have no anomalous signal? Or do I
> merge everything together?
> >
> > 3. Will the anomalous signal to 10 A be useful to do MR-SAD? I could
> solve the structure with MR but I wanted to be sure my ligand is there.
> >
> > Thanks.
> >
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