Just be careful when drawing conclusions from B-factors. If you look at the mathematical way that a B-factor modifies a structure factor, you can see that as a B-factor's numerical value increases, the corresponding structure factor's contribution to a calculated diffraction pattern is reduced. In other words, an error in the atomic model (such as in model bias errors) can be masked by B-factor refinement. Thus, if you want to draw conclusions from B-factors, one must assume that the all parts of a structure have been uniformly refined well (carefully and mostly correctly). Having at least several similar structures that were refined independently and give the same general result can add confidence to an observed trend in B-factors over different parts of a structure. Making a comparison between different structures refined independently is one reason for normalization of B-factors. TLS might indeed be a better way to go.
In any case, if you are exploring the relative mobility or degree of disorder of different parts of a structure, it would be a good idea to use an independent measure of flexibility in addition to the crystallographic result, such as H-exchange. -Daniel On Fri, Aug 10, 2018 at 5:21 AM, Gert Vriend <gerrit.vri...@radboudumc.nl> wrote: > TLS groups are a good way to reduce the R-factor without doing very stupid > things. They give a better fit of coordinates to the data, so, when done > well, you get a better description of reality without (hopefully) > over-fitting. Most times, I think, TLS groups are defined by the > experimentalist and it is rather easy to have some residues in a TLS group > that perhaps better should not have been in that group. In practice this > seems not to be a big problem, but when you are going to use TLS parameters > to compare mobility reduction it seems worth thinking about these problems. > > That's why we made the BDB (http://www.cmbi.umcn.nl/bdb/), a database in > which we (for about 80% of the whole PDB) calculated isotropic B-factors > for all atoms. Those isotropic B-factors might also not be the best thing, > but when studying mobility aspects of proteins they will work better than > either looking at TLS values or looking as residual B-factors. > > Obviously, the BDB holds data only for deposited PDB files, but if anybody > contacts me outside the list we might be able to help. > > Gert > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
