[phenixbb] Dual conformation on symmetry axis

Tim Gruene tim.gruene at psi.ch
Sat Feb 6 05:52:11 PST 2016


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Hi Pavel,

by artefact I mean density which is extremely difficult to interpret. When I 
worked in the K+ channels, especially the Tl version 1R3J, the difference 
density looks more pronounced than what I would have expected from ripples 
alone.
As small molecules do not need to follow the symmetry, they tend to be 
disordered. If this is multiplied by four on a four fold axis, it becomes much 
harder than anywhere else in the asymmetric unit.
I picked up from George Sheldrick that there are artefacts in the FT due to 
the proximity of special positions. As he usually knows what he is talking 
about, I trust his opinion, although there is a chance I misunderstood. Maybe 
you should discuss with him directly (I don't think he reads the phenixbb) for 
a clarification.

Cheers,
Tim


On Friday, February 05, 2016 07:35:58 AM Pavel Afonine wrote:
> Hi,
> 
> > density on symmetry elements usually displays artefacts and is difficult
> > to
> > interpret.
> 
> I've seen this rumor perpetuated so many times.. I think I can also say
> "Fourier maps show artifacts anywhere in the unit cell volume (including
> symmetry elements) that originate, for example, from: a) finite
> resolution and partial completeness of the data, b) errors in crystal
> structure model (model is always used as a source of phase information),
> c) measurement errors. These artifacts are difficult (and unnecessarily)
> to interpret in terms of atomic model.". Are symmetry elements somewhat
> special in this regard (that is one sees more artifacts on symmetry
> elements than anywhere else)? If this is the case, can someone provide
> convincing reasoning for this (not hand-waving!)?
> 
> Thanks,
> Pavel
- -- 
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Paul Scherrer Institut
Tim Gruene
- - persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5754

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