Although I would certainly try refining just Hg anisotropically and think that truncation ripples are very likely, you should also take into account that mercury derivatives are particularly sensitive to radiation damage. Often the Hg atoms have departed (but may still be in the vicinity) before the rest of the structure shows signs of the radiation damage. Since different reflections are measured at different times, this is general gives a mess in the difference map and there is not much you can do about it, though it might be worth refining the Hg occupancies. Normally one only refines against the native data and so does not see the mess.
George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Wed, 1 Aug 2007, Bart Hazes wrote: > 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 > > > -- > > ============================================================================== > > 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 > > ============================================================================== >
