By the way. Would it be possible to implement a wiki?
It would be beneficial, for a little "loser" user control, to write up some scratches, how to for example script up some analysis, of for example CPMG. I have looked into making a page at "http://nmrwiki.org/"; But they seem to have problems (for a long time now), so you can't edit anything. Best Troels Troels Emtekær Linnet 2013/5/30 Troels Emtekær Linnet <[email protected]>: > 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
