DebajyotiDutta escribió:
> Dear Sir,
>
> I have very little knowledge about anomalous dispersion method. The
> thing is that I have just started to deal with a case of SAD. I have
> consulted several text books to acquire knowledge about it though I
> have some queries. CCP4BB, I think is the best place to place my
> questions.
>
> 1.Is there any difference between Anomalous Dispersion and Anomalous
> Scattering?
No. Perhaps a distinction could be the case if compared to 'Anomalous
Diffraction' (which indeed appears to be the general experiment we
usually do with protein crystals anyway)...keeps the SAD acronym in any
case.
>
> 2.Sometimes I found that while searching for anomalous scatterer with
> SHELXD which give the coordinates of the scatterer in PDB format with
> occupancy more than 1. Why anomalous occupancy may be more than 1.
Not having other wavelengths measured (in contrast with MAD
experiments), there is no way to refine independently anomalous
scatterers' occupancies and the imaginary component of their atomic
structure factors (f''). So, most probably when you end up refining >1
occ's (physically awkward indeed), you're getting the info that the
input f'' should be refined to a lower value (perhaps not the tabulated
one : near-edge values can vary significantly owing to local
environment, anisotropy, oxydation state, etc) - of course this is also
the case when occupancies are less then 1, it's just that you don't look
at it with the same attention. For anomalous scatterer substructure
refinement purposes, anyway it's not a problem to leave occupancies
higher than one (mathematically, it will play just the same role as
reducing f'') (please correct me if I'm wrong here!)
>
> 3.I found that there is one plot (FPH – FP)/FP Vs Resolution indicate
> the isomorphism but how can I get this plot does SHELX has any option
> to print it.
Don't know in SHELX. SHARP does a great job in giving several tables
with useful information, including isomorphism (perhaps phasing power
and fogure of merit are a couple of ones that would be more powerful in
describing how sensible your anomalous scatterer substructure model is).
Indeed, one big advantage of MAD, and more so for SAD (less radiation
damage), is that non-isomorphism should be much less of a problem!
hth
best,
alejandro
>
>
> Thank you all for your time and reply to a beginners query in advance.
>
> Sincerely
> Debajyoti Dutta
>
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>
>
--
Alejandro Buschiazzo, PhD
Research Scientist
Laboratory of Protein Crystallography
Pasteur Institute of Montevideo
Mataojo 2020
Montevideo 11400
URUGUAY
Phone: +5982 5220910 int. 120
Fax: +5982 5224185
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