I missed that line from their paper: "The initial R20 rate was estimated as the lowest R2eff rate of each relaxation dispersion dataset."
They however do not address the R20 << min(R2eff) issue causing the grid search to be far from the region with the minimum. Correct me if I'm wrong there - maybe it's in their supplement or one of Peter Wright's other papers. Regards, Edward On 29 April 2014 23:20, Troels Emtekær Linnet <[email protected]> wrote: > Hi Edward. > > This feature is not totally un-known. > > It is used in GLOVE as well. :-) > > p. 280, J Biomol NMR (2013) 56:275–283 > dx.doi.org/10.1007/s10858-013-9747-5 > > Best > Troels > > 2014-04-29 15:14 GMT+02:00 Edward d'Auvergne <[email protected]>: >> Hi, >> >> I would maybe include a third paragraph saying that this is an >> experimental unpublished feature of the dispersion analysis. And that >> if R20 << min(R2eff), then the grid search will be performed in a >> region of the optimisation space quite distant from the true minimum. >> So if this is the case, then this feature should not be used. This is >> essentially to cover ourselves if a relax user tries this option but >> it causes their analysis to fail - because their analysis is different >> or performed in a non-standard way that we cannot foresee. We can >> then say that we said to use this at your own risk. The word >> "unpublished" is quite important for this. >> >> Regards, >> >> Edward >> >> >> >> On 29 April 2014 15:03, <[email protected]> wrote: >>> Author: tlinnet >>> Date: Tue Apr 29 15:03:58 2014 >>> New Revision: 22872 >>> >>> URL: http://svn.gna.org/viewcvs/relax?rev=22872&view=rev >>> Log: >>> Better formattting of text in user function. >>> >>> Feature request: #3151, (https://gna.org/support/index.php?3151) - User >>> function to set the R20 parameters in the default grid search using the >>> minimum R2eff value. >>> >>> Modified: >>> trunk/user_functions/relax_disp.py >>> >>> Modified: trunk/user_functions/relax_disp.py >>> URL: >>> http://svn.gna.org/viewcvs/relax/trunk/user_functions/relax_disp.py?rev=22872&r1=22871&r2=22872&view=diff >>> ============================================================================== >>> --- trunk/user_functions/relax_disp.py (original) >>> +++ trunk/user_functions/relax_disp.py Tue Apr 29 15:03:58 2014 >>> @@ -910,18 +910,19 @@ >>> >>> # The relax_disp.set_grid_r20_from_min_r2eff user function. >>> uf = uf_info.add_uf('relax_disp.set_grid_r20_from_min_r2eff') >>> -uf.title = "Set the initial guess for R20 in the grid search, to that of >>> the minimum R2eff points." >>> -uf.title_short = "Speed-up grid search." >>> +uf.title = "Set the R20 parameter values to that of the minimum R2eff >>> value." >>> +uf.title_short = "Set R20 from the minimum R2eff." >>> uf.add_keyarg( >>> name = "force", >>> default = True, >>> py_type = "bool", >>> desc_short = "force flag", >>> - desc = "A flag which if set to True will cause the R20 Values to be >>> overwritten if they already exist." >>> -) >>> -# Description. >>> -uf.desc.append(Desc_container()) >>> -uf.desc[-1].add_paragraph("Instead of making the grid search find initial >>> values of the R20 parameter, the minimum for the R2eff points are used >>> instead. For a 2 field cpmg experiment with model CR72, that would drop the >>> number of uniform grid search points from gridNr^5 to gridNr^3. For >>> standard 21 grid Nr, it would make the grid search 441 times faster.") >>> + desc = "A flag which if set to True will cause the R20 values to be >>> overwritten if they already exist." >>> +) >>> +# Description. >>> +uf.desc.append(Desc_container()) >>> +uf.desc[-1].add_paragraph("Set the R20 parameter values to that of the >>> minimum R2eff value. This user function will look through all R2eff values >>> per magnetic field strength, and find the minimum. This minimum is a very >>> good guess for the minimisation.") >>> +uf.desc[-1].add_paragraph("Instead of making the grid search find initial >>> values of the R20 parameter, the minimum for the R2eff points are used >>> instead. For example for a two field CPMG experiment with model CR72, that >>> would drop the number of uniform grid search points from 5D to 3D. For >>> standard 21 grid increments per dimension, it would make the grid search >>> 441 times faster.") >>> uf.backend = set_grid_r20_from_min_r2eff >>> uf.menu_text = "&set_grid_r20_from_min_r2eff" >>> uf.gui_icon = "relax.grid_search" >>> >>> >>> _______________________________________________ >>> relax (http://www.nmr-relax.com) >>> >>> This is the relax-commits 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-commits >> >> _______________________________________________ >> 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 _______________________________________________ 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
