Hi, The relax paper has been submitted but hasn't been accepted yet. It is one of a series of four papers submitted together which discuss the different optimisation aspects within relax. Labelling them Papers I, II, III, and IV, the one presenting relax is Paper IV. Models m0 to m9 are presented in Paper I (models m10 to m39 haven't been discussed). Models tm0 to tm9 are presented in Paper III. Essentially Paper I presents and compares the optimisation algorithms used in relax, and compares them with Dasha and Modelfree4. Paper II is a bit of a review of the model-free field with a twist - it recasts the entire problem using set theory and presents the universal set and universal solution (these new concepts are key to the new model-free protocol presented in Paper III). Paper III re-derives the Brownian rotational diffusion equations and significantly simplifies them from an optimisation perspective, presents equations for collapsing the symmetries of the diffusion parameter space, and presents the new model-free optimisation protocol coded into the 'full_analysis.py' script. Paper IV presents relax by reanalysing a recent model-free publication.
In summary for relax: Paper I = the optimisation algorithms of the program; Paper II + III = the new model-free protocol in 'full_analysis.py'; Paper IV = relax. The titles are: Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free space. Optimisation of NMR dynamic models II. Set theory formulation of the model-free problem and Kay's model-free paradigm. Optimisation of NMR dynamic models III. Derivation of the Brownian diffusion correlation functions and a new methodology for the dual optimisation of the model-free parameters and the diffusion tensor. Optimisation of NMR dynamic models IV. A new software program for the study of protein dynamics through NMR relaxation data analysis - relax. How you cite the ones you wish to cite would probably depend on your journal style/convention (for example you may need the journal which these were submitted to). The authors on all four would be "d'Auvergne, E. J. and Gooley, P. R.". Between the submission and the proofing stages of your publication hopefully this series will progress to 'accepted', 'in press', or published. I could privately send a draft copy of any of these if you wish. In addition to these four papers the AIC (or BIC, cross validation, bootstrap, etc.) model selection and the important 'eliminate()' user function are discussed in: d'Auvergne, E. J. and Gooley, P. R. (2003). The use of model selection in the model-free analysis of protein dynamics. J. Biomol. NMR, 25(1), 25–39. d'Auvergne, E. J. and Gooley, P. R. (2006). Model-free model elimination: A new step in the model-free dynamic analysis of NMR relaxation data. J. Biomol. NMR, 35(2), 117–135. Cheers, Edward On 11/6/06, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
Hi Edward- Do you have a paper on relax in the pipeline to be published soon? Also, do you have any references to other papers discussing the list of models found in: Chapter 10 -- ALPHABETICAL LISTING OF USER FUNCTIONS 10.2.29 model free.select model (m0-m39, tm0-tm39) Thanks, Doug
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