Hi Klemens,
As friends of the Fourier transform we hate to see it truncated.
Although others don't think this is your problem I personally think it
very well may be. To get a truncation effect you must first have
truncated your data.
- Is the I/SigI of your highest resolution data in the 1-2 region or
more like 3 or higher?
- Second, truncation ripples are just that oscillating negative and
positive shells of density around the central atom density. The first
negative ripple will be strongest strongest, but if you contour lower
you may be able to see a second positive one at a little greater
distance (you do say "ripple layers" so you may already have spotted it).
The bad news is that as far as I know there is no remedy. The ripples
are not due to your model so no refinement trick can help you out (when
you would have perfect experimental phases you would still see the ripples).
You can apply a de-sharpening B-factor to the data to weaken the high
resolution terms. That would dampen the ripples but also harm the rest
of your data.
The good news is that the ripples don't really affect your model or the
biological conclusions you derive from it. In the paper you will just
have to confess that you didn't do your data collection properly and
then get on with the show. Unfortunately, there are far too many papers
with native data sets that do not collect data to the diffraction limit.
I think we need a "Save the Native Structure Factor" action group to
protect the endangered high resolution native reflections. This is
ALWAYS bad (the exception is for experimental phasing data sets) but
only when you have a heavy atom do you see the ripples (I have had it
myself with an ion as light as copper).
W.r.t. Kay's reply I think the argument does not hold since it depends
on how badly the data is truncated. E.g. truncated near the limit of
diffraction will give few ripples whereas a data set truncated at I/SigI
of 5 will have much more servious effects.
Bart
Kay Diederichs wrote:
Klemens Wild schrieb:
Dear friends of the Fourier transform,
I am refining a structure with 2 adjacent Hg atoms bound to cysteines
of different monomers in the crystal contacts, which means I need to
refine them as well. While the structure nicely refines (2.2 A data),
I do not get rid of negative density ripple layers next to them (-10
sigmas). My question: is this likely due to anistropy of the soft
mercury atoms (anisotropic B refinement decreases the ripples) or is
this likely a summation truncation effect prominent for heavy atoms?
Can I just anistropically refine the mercuries while I keep the rest
isotropic? Never saw this in a PDB. Suggestions are very welcome.
Greetings
Klemens Wild
Dear Klemens,
the height of a Fourier ripple should not exceed about 12% of the peak
itself (just look at the maxima of sin(x)/x which is the Fourier
transform of a truncation function). In reality it should even be lower
due to the average temperature factor being >0.
Thus, only if your Hg peaks are on the order of 80 sigmas (which I
doubt) it appears justified to consider the 10 sigma peaks as ripples.
It is more likely that aniso refinement should be able to get rid of the
"ripples".
best,
Kay
--
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Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone: 1-780-492-0042
fax: 1-780-492-7521
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