Hi Troels, The relaxation dispersion GUI in relax is now fully debugged and functional. Well as far as I can tell anyway. Enjoy!
Regards, Edward On 30 May 2013 17:34, Edward d'Auvergne <[email protected]> wrote: >> You are very productive! and I am stunned to see the development >> so fast. :-) > > Well, I'm sorting out the code for myself specifically for my own > R1rho analyses. I'm guessing you are interested in the CPMG side of > things. > > >> I think you are hitting "the nail" with the current development of relax. > > There's not much left to finish with the base infrastructure. As for > adding new models, that's a different, but relatively easy story. The > numerical integration of the Block-McConnell equations might take more > effort to add but, as all the infrastructure is in place, it shouldn't > be too hard. Integrating with the other softwares (input file > creation, execution, and reading of results - for NESSY, CPMGFit, > ShereKhan, Catia, Chemex, etc.) will be a continual work in progress. > It will be advanced when someone needs it, this is currently myself to > fully automate the comparison between all the different dispersion > programs simply for sanity purposes. > > >> At the moment the "hardest/time consuming" part for students in our lab, is >> the analysis of the >> results. We have a good workflow from recording and peak assignment. >> But from there, it gets more tricky. > > I know this problem well :) > > >> Most of our analysis part is based on "home made" scripts for Igor >> Pro/Matlab. > > Ah, the code for the dispersion models shouldn't be too difficult to > port into relax if you already have Matlab code in place! > > >> They come a long way for most of our analysis. >> The problem is that for a "beginner" there can be a "high energy barrier" to >> start >> using these scripts. Not mentioning "license problems", installation and >> such. >> And if you have to make some peak adjustments, then the whole analysis >> should be performed again. >> For a "trained" this takes some hours, but for un-trained, it can take a day >> or two. > > I understand this, and this is one useful advantage of a GUI. I don't > know how you would avoid having to redo a full analysis if the input > data is changed though, except that maybe you could have a relax save > file for the GUI analysis and slightly tweak the data already within > relax, and the rerun the full analysis. > > >> We have been looking for other software for CPMG. >> At least to "quickly" try to match our scripts values. (Here Nessy seemed >> very interesting, but very buggy) > > I am now the maintainer of NESSY so I can fix some of the trivial > bugs. I have been doing this for a few annoying bugs, for example > see: > > https://mail.gna.org/public/nessy-commits/2013-05/threads.html > > However finding the big bugs and improving the optimisation will not > be possible for me at the moment. > > >> But concerns about installation, development, and even a "harder" interface >> than Igor Pro/Matlab, stopped us. >> We(as in me) are at the moment matching some test results at the Sherekhan >> server, after making >> a input converter to Sherekhan. That seems to be very easy, and promising. > > relax now has this as well in the relax_disp.sherekhan_input user > function. You can access this from both the prompt/script mode and > the GUI. I've noticed though that the ShereKhan numerical integration > of the Block-McConnell equations is currently problematic and the poor > little tiger just runs forever! > > >> I am very impressed with relax. Mostly because the GUI can take care of >> novices, and there exist the possibility to >> script it all up for extensive analysis. >> It's free, and I was able to install it on Windows/Linux without to much >> fuss. > > Cheers! That is exactly what the relax developers have tried to create: > > - the GUI is really for those who don't have much interest in the > theory and just want quick, idiot-proof results from a blackbox (i.e. > perfect for undergrads), > - the prompt/script mode is for power users with interest in the NMR > theory and analysis, > - the prompt/script mode in combination with the relax library > functions is to be a replacement for Mathematica/Matlab for those who > want to live on the cutting edge. > > >> If I want to try some of our data, is the GUI ready for trying? > > There are a few minor bugs I have to sort out first. For example with > the error analysis for peak heights. It should be ready for the > 'R2eff' and 'LM63' models soon though. Still, right now you can do > everything except for clicking on the 'Execute analysis' button. I > hope it won't take too long. > > Regards, > > Edward > > > > >> 2013/5/29 Edward d'Auvergne <[email protected]> >>> >>> Hi, >>> >>> Troels, you might be interested in the following comparison. The >>> reviving Sebastien Morin's relaxation dispersion branch in relax is >>> now complete. The relax_disp branch can now correctly optimise one of >>> the dispersion models, that of Luz and Meiboom 1963 for 2-site fast >>> exchange for CPMG-type experiments. This does not implement the >>> gradients or Hessians yet, and parameter constraints are still to be >>> added. But nevertheless relax can find the correct parameter values. >>> This should be a good test of the dispersion code in relax as the >>> addition of other models - such as that for R1rho data, more >>> complicated models for CPMG-type data, and numerical integration of >>> the Bloch-McConnell equations - should be trivial after that >>> (requiring only 20-50 lines of new code, not counting comments and >>> docstrings). >>> >>> Through relax user functions, I can now generate the input for CPMGFit >>> and NESSY. These are the relax_disp.cpmgfit_input and >>> relax_disp.nessy_input user functions. We can now also execute >>> CPMGFit within relax using relax_disp.cpmgfit_execute. This can be >>> completed later, but the idea is to follow the concept of model-free >>> user functions: >>> >>> dasha.create >>> dasha.execute >>> dasha.extract >>> palmer.create >>> palmer.execute >>> palmer.extract >>> >>> These are for the Dasha and Modelfree4 programs respectively. >>> Implementing the 3 user functions for creating input files, executing >>> the program in-line, and extracting the results from the program's >>> output will allow relax to use external programs as optimisation >>> engines. This is useful for comparing the results from different >>> programs and really eliminating all bugs from the dispersion field. >>> >>> Back to the comparison, I have used Flemming Hansen's 500 and 800 MHz >>> CPMG data from: >>> >>> Hansen, Vallurupalli & Kay, 2008, JPhysChemB, 112: 5898-5904. >>> >>> which he donated to Seb to be added to relax (located in >>> test_suite/shared_data/dispersion/Hansen/). Looking at a single >>> randomly chosen residue (number 70), I see different results from the >>> 3 programs: >>> >>> Param relax NESSY CPMGFit >>> R2 (500) 6.806 7.639 6.866 >>> R2 (800) 6.679 7.387 6.866 >>> phi 1.259e-13 0.259 1.226e-13 >>> phi (500) 31464.605 26292.031 30644.496 >>> phi (800) 80549.390 67307.598 78449.180 >>> kex 4763.249 3906.180 4.683 >>> tau 4.199e-05 5.120e-05 0.427 >>> chi2 106.393 156.446 106.471 >>> >>> tau = 2/kex (I think that CPMGFit works with ms units). >>> >>> Obviously NESSY is not doing so well (likely due to using the horribly >>> buggy scipy optimisation code) and relax and CPMGFit find the same >>> result for this model. The slight difference between relax and >>> CPMGFit is that it looks like CPMGFit assumes the same R2 value for >>> all static fields - which I think would be a little strange, >>> especially if fast internal motions are also present for that spin >>> system. >>> >>> Therefore I believe that this relax branch is in a state to accept >>> code for the other models. The backends for the >>> relax_disp.cpmgfit_input and relax_disp.nessy_input could be also >>> modified to handle these new models to allow for rigorous comparisons >>> and debugging. The dispersion infrastructure should no longer have >>> any large changes, so feel free to start playing. >>> >>> 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 >> _______________________________________________ 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
