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]
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......................
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