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 -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
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