Does anyone know what the record is for "most reflections per atom?"
JPK On Fri, Apr 8, 2011 at 8:06 AM, Ian Tickle <[email protected]> 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: [email protected] *******************************************
