Hi Kenneth, > I know that TLS is a group B factor for regions of proteins that are moving > the same.
You have to be a bit careful here: first B factors do not necessarily imply motion, they imply displacement (i.e. it could mean static displacements which just vary between unit cells). That's why they are called 'displacement parameters' (as in 'ADP' if it's anisotropic). Second, 'moving the same', or even 'being displaced the same' carries the connotation that you are getting information about correlated _motion_ or displacement, which is not correct either, though it may well be one interpretation of the results. Strictly TLS only gives you information about correlated _dispersion_ (in the strict sense of dispersion as 'variance'), not correlated _displacement_, though you may well interpret correlated dispersion as correlated displacement (i.e. other interpretations of the results may fit the data equally well). The difference between displacement and dispersion is illlustrated by considering a group of atoms in a molecule: if these atoms all have identical instantaneous displacements at all times, as though they were rigidly connected, that's correlated displacement. If the atoms are moving completely independently (i.e. their displacement vectors are in general all different both in direction and magnitude), but they happen to all have the same ADPs (which are a time/lattice average of the squared displacements), that's correlated dispersion. Of course in practice you will see all shades between these two extremes. > It is used in low res structures. But at what resolution does one begin > anisotropic, i.e > individual aniso for each atom, and leave TLS out. Depends what you mean by 'low'. You can use individual ADPs when you have a sufficient data/parameter ratio, which as a rough guide I would say is around 1.5 Ang., though you would still need to use ADP restraints (as in Shel-X) at resolutions between 1.5 and say around 1 Ang (at what point you can safely drop ADP restraints beyond 1 Ang is a matter of taste). > Or can one still use TLS to first > compensate for large motions and then dampen down the individual atoms with > aniso ADP? Not sure what you mean by 'dampen down': do you mean 'restrained'? For the purposes of refinement it would be tricky to do this in practice because TLS and ADP parameters are not independent. The first thing the refinement program does with the TLS parameters is calculate the equivalent ADPs and use those in the SF calculation, though of course the results are ultimately still expressed in terms of changes in the TLS parameters. A better way of doing this would be to use only ADPs in refinement, and interpret the results post-refinement as TLS + 'residual' ADPs. This is how TLS was used years ago for small molecules before refinement of TLS parameters directly was coded (though the residual ADPs were usually viewed as just 'random error'). The problem here is what you call 'residual', i.e. because they are not independent, you can interpret the results as either correlated displacement or correlated dispersion, and the data aren't going to help you to decide which is the more correct interpretation. > If both the aniso and TLS are used, how does a person interpret the results? > What programs > are there to see just what is large body motions and what is atoms. I've never tried this, so I can't say if it would be a useful exercise or not. I think I would stick to the TLS + individual _Biso_ model: that is already hard enough to interpret! Cheers -- Ian
