btw, this thread has one of my favorite titles ever... JPK
On Tue, Oct 9, 2012 at 4:11 AM, Eleanor Dodson <[email protected]>wrote: > 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 > > > > > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: [email protected] *******************************************
