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
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