Well. Most of my values for kA are 2-6. Which seems fine.
But I also got a negative kA value and one of thousands. And my dw values are also strange. I have to look into which units the paper report data in, and if there are more supporting information I can look at. Let me return to this, when I have setup a test-suite. Best Troels Troels Emtekær Linnet 2013/9/4 Edward d'Auvergne <[email protected]>: > Hi, > >> Is there a way to see the start value for a variable in a CPMG model fit. ? > > Not in the auto-analysis, as there are no starting values. > > >> When using the auto_analysis, : >> >> -------- >> from auto_analyses.relax_disp import Relax_disp >> Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle, >> results_dir=results_directory, models=MODELS, grid_inc=GRID_INC, >> mc_sim_num=MC_NUM, modsel=MODSEL) >> -------- >> >> I see no options to modify the grid_search ? > > Currently the only option is to change the number of grid increments. > For the auto-analysis, changing the other options is not such a good > idea. For a custom dispersion analysis, you are free to do anything. > The auto-analysis is limited to help users who are only interested in > a result whereas a custom analysis is unlimited in what can be done. > Actually if the user changes the grid increments to be below 7, that > could be fatal for the results. The defaults in relax must allow the > minimum to be found in absolutely all cases, and the current defaults > should do that. > > >> When I grep the logfile, I see each model use a grid_search >> >> grid_search(lower=None, upper=None, inc=21, constraints=True, verbosity=1) >> http://www.nmr-relax.com/api/3.0/pipe_control.minimise-module.html#grid_search >> >> Is it possible change the lower and upper bonds for the grid_search, >> or should one run all the commands manually? > > These cannot be changed in the auto-analysis. The reason for this is > that relax provides defaults which will work in all cases. To see > this, look at the _grid_search_setup() method in the > specific_analyses.relax_disp.api module. The user should really not > touch these upper and lower bounds as they might cause the minimum to > be missed. A power user not using the auto-analysis can play with > such things, but definitely not a normal user. However a power user > should probably not change these anyway. > > Note that the constraints will remove half of this grid due to the pA >> pB constraint. The other constraints remove other parts of the > grid. But the grid is only used to find a rough starting point for > optimisation so that the minimiser can easily find the minimum. This > is not a question of local verses global minima, as there is only one > minimum for the 2-site models (analytic and numeric). The problem is > that if you start too far from the minimum, due to the non-linearity > of the parameter space the optimisation algorithm may not be able to > reach the minimum. This is why a grid search is almost always used as > the starting point for mathematical optimisation. There are other > techniques that can be used, but they are similar in concept - you > simply need some algorithm pick a rough position close to the minimum. > Then you use the optimisation algorithm to refine and find the exact > values. > > So you start with no parameter values, use the grid search to find a > rough starting position, then use the simplex optimisation algorithm > to refine the parameter values. The rough parameter values after the > grid search are of no scientific interest, so these numbers are never > output (apart from the printouts from the grid search itself). The > values are stored in relax to be used by the subsequent minimise() > user function, and then they are overwritten by the higher precision > parameters. > > >> I could grep the logfile after an Autoanalysis to see the commands: >> http://wiki.nmr-relax.com/Grep_log_file >> and then change the grid search parameters. > > What is the purpose of changing these? Are the defaults not good enough? > > >> --- >> On another note. >> >> Would it be possible to write the starting values into the table 10.1 >> in the relax_disp >> manual? > > No, because there is no such thing as a starting value ;) > > Regards, > > Edward _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
