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== About the protocol ==
'''Model I - 'local_tm''''<br>
This will optimise the diffusion model whereby all spin of the molecule have a local tm value, i.e. there is no global diffusion tensor. This model needs to be optimised prior to optimising any of the other diffusion models. Each spin is fitted to the multiple model-free models separately, where the parameter tm is included in each model.
'''Model II - 'sphere''''<br>
This will optimise the isotropic diffusion model. Multiple steps are required, an initial optimisation of the diffusion tensor, followed by a repetitive optimisation until convergence of the diffusion tensor. In the relax script UI each of these steps requires this script to be rerun, unless the conv_loop flag is True. In the GUI (graphical user interface), the procedure is repeated automatically until convergence. For the initial optimisation, which will be placed in the directory './sphere/init/', the following steps are used:
* The model-free models and parameter values for each spin are set to those of diffusion model MI.
* The local tm parameter is removed from the models.
* The model-free parameters are fixed and a global spherical diffusion tensor is minimised
* For the repetitive optimisation, each minimisation is named from 'round_1' onwards. The initial 'round_1' optimisation will extract the diffusion tensor from the results file in './sphere/init/', and the results will be placed in the directory './sphere/round_1/'. Each successive round will take the diffusion tensor from the previous round. The following steps are used:
** The global diffusion tensor is fixed and the multiple model-free models are fitted to each spin.
** AIC model selection is used to select the models for each spin.
** All model-free and diffusion parameters are allowed to vary and a global optimisation of all parameters is carried out.
== See also ==
[[Category:Tutorials]]
[[Category:Model-free_analysis]]
