Uhhh, that is great. :-) Looking forward to try!
Troels Emtekær Linnet 2013/5/30 Edward d'Auvergne <[email protected]> > > 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
