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
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