This is interesting. In principle m and D should provide an optimum map, and at high resolution they do a reasonable job. The answer about occupancy is a good point.
You don't say what resolution your data is at, but maybe it is rather low? I suspect that below ~ 3A the estimates of both m and D are somewhat unreliable - they are fitted to resolution curves and are influenced severely by scaling problems, all of which are more serious at low resolution. What about consulting Garib! He must be near by.. Eleanor On 4 Oct 2012, at 20:17, Israel Sanchez wrote: > Hello everyone, > > I would like to share my experience with one dataset and request some advice > on which is the best way to prove a conformational change seen in a density > map. > > The first issue arose when we were looking for an extra ribosomal factor > added to a crystalized ribosome. After careful data collection and refinement > (I/sigma last shell 1.2, 3.1A and CC1/2 around 22%) the sigma-A-weighted maps > 2mFo-DFc and Fo-Fc does not show any clear difference density that we could > interpret as the expected factor. Interestingly, a computed map with > coefficients 3mFo-2DFc started to show some features that clearly could be > explained as a fragment of the factor. The density improved even more with a > B-sharpened map. We have seen this behavior before and I was wondering if > someone else is using this kind of maps and may could explain the reason > behind this density improvement. Is it a crazy idea to go even higher like > 4mFo-3DFc? > > The second query has to do with which is the best way to prove that a > conformational change is present in an specific residue (in this case and RNA > base) in your structure. To my knowledge, a classic omit map with simulated > annealing would do the job regarding removing the model bias. Actually, I > found an interesting alternative in PHENIX called a Kick map, were a series > of maps computed from a ramdoinised set of models yields a averaged map > ideally free from model bias. Does anyone has a preference for any of those > schemes? Are there more alternative to prove a conformational change in a > model phased with a molecular replacement solution? > > Thank you very much in advance. > -- > Israel Sanchez Fernandez PhD > Ramakrishnan-lab > MRC Laboratory of Molecular Biology, > Hills Road, Cambridge, CB2 0QH, UK > >
