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Re: [ccp4bb] difference density ripples around Hg atoms |
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CCP4bb navigationCCP4bb <-- 2007 <-- August 2007 <-- 01 August 2007Subject: Re: difference density ripples around Hg atoms From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE Date: 2007-08-01 > 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: Kay.Diederichs@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz CCP4bb navigationCCP4bb <-- 2007 <-- August 2007 <-- 01 August 2007 |
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