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As only small part of the molecules is shown and it appears to be in poly-alanine representation, more interesting
thing may happened apart of "numerical instabilities" of Fourier transform. These can be mutually exclusive conformations that brake local symmetry but preserve overall symmetry.
The alts penetrate forbidden region of the symmetry, but only from one molecule. 
I have seen such things. BTW what program was used to calculate maps?
FF
Dr Felix Frolow   
Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: [log in to unmask]
Tel:  ++972-3640-8723
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On Nov 5, 2012, at 12:22 , Tim Gruene wrote:

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Dear Shutong Xu,

one often finds artefacts on special positions. As far as I
understand, these are numerical 'instabilities' or artefacts rather
than of chemical origin.

Best,
Tim

On 11/05/2012 10:50 AM, Crystal Xu wrote:
Dear all,

I am now determining a structure at 2.2 A resolution. The space
group is C2, and there is only one molecular in an ASU. During the
refinement, some weird electron density appears right on the
two-fold axis. Does anyone have any idea what could this be? Thanks
a lot. Best regards

Shutong Xu


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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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