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On Thursday 22 June 2006 09:38 am, Kaj Stenberg wrote: > > I experienced exactly the same problems. In my case the solution was > to use the TLSMD-server > http://skuld.bmsc.washington.edu/~tlsmd/index.html > > After continuing with files obtained from there all problems > disappeared. I could never figure out why. Thanks for the plug for TLSMD :-) Yes, using the TLSMD analysis to define the starting point for TLS refinement can be a good idea even if you somehow already know what TLS groups you would like to refine. This is because the files generated by the TLSMD server describe not only the nature of the TLS model (which atoms are in which TLS group) but also the current value of the TLS parameters for that group. So you are basically starting the refinement with a set of parameters known to describe the B factors in your current structural model. By contrast, if you begin TLS refinement with an "empty" model - one that describes the atoms in each group but sets no starting point for the corresponding TLS parameters - then you are trusting automated refinement to converge back to a reasonable state from a starting point that is far away from describing the B factors in your current model. Ethan Merritt > > Kaj Stenberg > > On Thu, 22 Jun 2006, Gina Clayton wrote: > > I am having major problems with a TLS refinement. . .One of the > > things that is happening is that the B factors are being assigned > > to 2.0 with rfactor 80 and FOM 0.1 for some of my groups (CA or > > whole molecules) during say cycle 7 of the refinement. So I tried > > less cycles (did not work) or with just the whole molecule and CA > > only. Now the output is some of the B factors are assigned values > > too low i.e 2 to 8 whilst others seem reasonable. The latter I only > > got to work using a TLS refined PDB in restrained refinement with a > > fixed TLS from the first TLS I performed. When the TLS refinement > > goes bad the TLS matrix values leap to very high numbers i.e. 220 > > or something. > > > > I am using refined structures (CNS refined). Has anyone ane ideas > > that may get this running? For instance should I "jumble" my > > molecule up again in a simulated anneal i.e. is it becuase my model > > is refined already and I am over refining? Or is it becuase the > > model is too small each monomer is about 15-18kDa? > > > > thanks for any guidance > > > > Gina -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle WA
