Does anyone know what the record is for "most reflections per atom?"
JPK
On Fri, Apr 8, 2011 at 8:06 AM, Ian Tickle <[log in to unmask]> wrote:
> 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
>
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: [log in to unmask]
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