I'd be surprised if the model phases were introducing bias into an
anomalous difference map (they might be adding noise, but that's another
story). I've also never seen feedback in model-phased anomalous
difference maps (experimental-phased anomalous difference maps can have
pretty bad feedback).
Have you tried cutting the known Se sites out of your map? Or phaser
sas residual maps?
Pete
Jacob Keller wrote:
> Update:
>
> I tried more anomalous maps, this time with the originally-deposited
> data at 1.8 Ang (mine were similar, substrate-soaked crystals) and
> phases from the refined model, and the Se sites are now ~40-50 sigma,
> and there is still totally nothing at the Cl and S sites, even though
> in 2Fo-Fc the Cl is ~9 sigma, and the S is 8 sigma (the Se is ~15
> sigma). If it has reasonably-high electron density, shouldn't it have
> at least some anomalous scattering? I am wondering whether somehow the
> model phases are biasing the map, but I can't really imagine how that
> would be...
>
> JPK
>
>
> On Thu, Sep 1, 2011 at 3:15 PM, Bosch, Juergen <[log in to unmask]> wrote:
>> Where in refinement of your model are you ?
>> At an early stage I wouldn't be surprised to only see SeMets but once you've
>> refined your structure and go back to calculate an anomalous map with the
>> improved phases you might double your signal for SeMet and start seeing
>> sulfurs.
>> An alternative explanation, you've blasted your crystals at the synchrotron
>> and the remaining anomalous signal is too weak to show the sulfurs.
>> Just two thoughts,
>> Jürgen
>> On Sep 1, 2011, at 4:03 PM, Jacob Keller wrote:
>>
>> Dear Crystallographers,
>>
>> I recently have been working with a 2.5 Ang SeMet peak wavelength
>> dataset which contains 2 cys's and also a couple of bona fide Cl ions
>> (reasonable b-factor/site is semi-buried/water does not work). In the
>> FFT anomalous difference map using PhiC from the refined model and
>> Dano, I can see the MSE's at ~10 sigma, but no Cl ions, even though Cl
>> should have f" = ~0.3 versus Se's f" = ~4, and no S's in the cys,
>> despite f" = 0.23e. There is really no anomalous peak at all--is it
>> just the smallness of the signal, or are the Se's somehow "swamping
>> out" the other signal? Perhaps the phases are tainted by the presence
>> of semet in the model?
>>
>> Looking for suggestions,
>>
>> Jacob Keller
>>
>> *******************************************
>> Jacob Pearson Keller
>> Northwestern University
>> Medical Scientist Training Program
>> cel: 773.608.9185
>> email: [log in to unmask]
>> *******************************************
>>
>> ......................
>> Jürgen Bosch
>> Johns Hopkins University
>> Bloomberg School of Public Health
>> Department of Biochemistry & Molecular Biology
>> Johns Hopkins Malaria Research Institute
>> 615 North Wolfe Street, W8708
>> Baltimore, MD 21205
>> Office: +1-410-614-4742
>> Lab: +1-410-614-4894
>> Fax: +1-410-955-2926
>> http://web.mac.com/bosch_lab/
>>
>>
>>
>>
>>
>
>
>
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