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On Sunday 27 August 2006 05:05 am, Jorge Iulek wrote: > > > > In my experience, even using just one TLS group per monomer has > > often led to a significant (>1%) decrease in Rfree, so it's not > > even always necessary to find creative ways to chop molecules into > > smaller groups. > > Yes, amongst the "different models" I meant the "basic" one > considering each monomer separately. But it is good to reinforce > that, maybe that does not get clear. Anyway, some automation is > gotten at the > http://skuld.bmsc.washington.edu/~tlsmd/index.html server. The common case is that the largest increment drop in R/Rfree comes from treating the entire molecule, monomeric or multimeric, as a single TLS group. This essentially acts to account for the overall vibrational flexibility allowed by the lattice packing. Subdividing a multimer into separate TLS groups for the individual subunits may or may not gain you much additional improvement, because generally the subunits within a multimer are much more tightly coupled than are the adjacent molecules in the crystal lattice. You start getting larger gains again by breaking down individual subunits into domains/subdomains/loops with internal hinge flexibility. This is the analysis performed by the TLSMD server. Of course there are exceptions. Some crystals are "rocks", and have such extensive inter-molecule lattice contacts that you gain nothing by applying a TLS model to the whole molecule. In such a case you may nevertheless still benefit from multi-group TLS models, since even though the bulk of each molecule is tightly constrained by the lattice, individual loops or subdomains may still be free to hinge relative to the body of the protein. Conversely, you sometimes find loose lattice packing of a very compact protein. In this case you may find substantial benefit from whole-molecule TLS, but little to no additional improvement from trying to break the molecule into smaller pieces. TLSMD server: http://skuld.bmsc.washington.edu/~tlsmd/ -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle WA
