Hi Seb, Don't worry about my questions about Flemming Hansen's data in relax, I just looked at his original paper (http://dx.doi.org/10.1021/jp074793o) and remembered again that this data uses the formula:
R2,eff(νCPMG) = -1/Trelax * ln(I1(νCPMG)/I0) So this requires no exponential curve-fitting, just a simple direct calculation prior to fitting the dispersion curves. Regards, Edward On 11 April 2013 15:55, Edward d'Auvergne <[email protected]> wrote: > Hi Seb, > > Thanks for the response. As I have some R1rho dispersion data I am > measuring and as NESSY is in no state to handle this data, I decided > to resurrect your branch. This was for my own personal use and is the > fastest way for me to process the data. This didn't take much effort. > The changes I needed to perform were: > > - port all of your commits to a new dispersion branch (the old branch > was too out of date), > - enable clustering of spins (requiring large infrastructure changes), > - the outputting of 2D Grace curves of R2eff values (for example for > the dispersion curves), > - a better, more flexible design of the target function class to allow > different diffusion equations, > - shifted the dispersion equation Python code, converted from your > original C code, to lib/dispersion/equations.py (that was trivial), > - some trivial Python 3 fixes, > - some updates of your old code for the newer relax design, > - some new, quite simple user functions (relax_disp.spin_lock_field, > relax_disp.relax_time) and modified relax_disp.cpmg_frq, > - created a basic 'auto-analysis' which will enable a GUI front end to > be created for the dispersion analysis (probably only requiring 1-2 > days of work). > > This was really only a few days of work. I do not have your fast and > slow 2-site equations for CPMG data running yet and had a question > about the dispersion data Fleming Hansen sent you. I am looking at > making your system tests for fast and slow 2-site exchange pass. For > this, would you be able to forward me the original email from Fleming > which contains the data? > > The reason is because the data in relax test suite appears to be > incomplete. Unless the data is the R2eff values already obtained form > the peak intensities, but the numbers in the *.in files are on the > order of 1000 so they must be peak intensities. But there should be > one peak intensity for each relaxation time to have exponential > curves. The current way to analyse this data is the same as in the R1 > and R2 analysis, in that relax will read in peak intensities from > Sparky, NMRView, XEasy or generic peak lists, and optimise both the > exponential curves together with the chosen dispersion model. If you > can remember, I was also wondering how you created the *.in_sparky > files with chemical shifts? The data doesn't appear to be the same as > that which is distributed with CATIA > (http://pound.med.utoronto.ca/~flemming/catia/), but it looks like the > *.in files correspond to the *.out files in the > Examples/Ncp_CW/data_500 and Examples/Ncp_CW/data_800 directories. If > you could, in your spare time, dig out this old information that would > be much appreciated. > > Cheers, > > Edward > > > > On 3 April 2013 22:16, Sébastien Morin <[email protected]> wrote: >> Hi all, >> >> Thanks Edward for keeping me posted on this topic. >> >> It is very long ago that I started implementing the relaxation dispersion >> code in relax, however with very little success. >> >> Although I felt this was important, changing project and missing time were >> major reasons for giving up. I ma happy to learn that Paul might be able to >> really complete this task, making relax useful for a broader set of >> analysis. >> >> Relaxation dispersion experiments are increasingly used, often using >> in-house and/or black box program. An open source transparent and highly >> dynamic program implementing relaxation dispersion codes would be very much >> welcome ! >> >> If I can be of any help (although I doubt it), please feel free to contact >> me..! >> >> Best, >> >> >> Sébastien >> >> >> On 13-03-23 3:20 PM, Edward d'Auvergne wrote: >>> >>> Hi Paul, >>> >>> I would like to help you with the conversion of your Matlab code for >>> the numerical integration of the Bloch-McConnell equations to Python >>> and its incorporation into an existing open source project, as you >>> discussed on the NESSY development mailing list: >>> >>> https://mail.gna.org/public/nessy-devel/2013-03/msg00000.html >>> >>> and in private messages. Note that I am the caretaker of the NESSY >>> project and am not too familiar with the codebase, so I would not be >>> able to help you too much. Though I should be able to point you in >>> the right direction when needed. You should also note that there are >>> some major bugs which you would need to be aware of, as they might >>> influence your endevours: >>> >>> https://gna.org/bugs/?group=nessy >>> https://mail.gna.org/public/nessy-users/2012-12/msg00002.html (the >>> response by James Nyirenda to that message is not correct). >>> https://mail.gna.org/public/nessy-users/2012-12/msg00000.html >>> >>> Importantly, the R1rho side of NESSY is non-functional and requires >>> major surgery: >>> >>> https://mail.gna.org/public/nessy-users/2012-06/msg00010.html >>> >>> However I didn't have and still don't have the time to refactor this >>> codebase: >>> >>> https://mail.gna.org/public/nessy-users/2012-06/msg00011.html >>> >>> The reason I am writing on this list is because I would like to point >>> to you a large quantity of work already present in relax specifically >>> for relaxation dispersion. Sebastien Morin has an almost complete >>> relaxation dispersion analysis coded into relax for the optimisation >>> of the parameters of the 2-site model using the analytically derived >>> equations. The code is in the relax_disp relax branch: >>> >>> http://svn.gna.org/viewcvs/relax/branches/ >>> >>> Also, Dr Flemming Hansen helped us by giving us some of his CPMG data >>> to use as test data for the test suite. You can see it in the >>> test_suite/shared_data/curve_fitting_disp/Hansen/ directory of the >>> branch at: >>> >>> >>> http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/curve_fitting_disp/Hansen/ >>> >>> The readme file explains the data. Note that the branch is now quite >>> old. Therefore to use it I would suggest that a new branch is created >>> and each of Sebastien's commits be ported to the new branch. I would >>> also suggest not using C code for the relaxation dispersion equations. >>> >>> Because relax has active developers and has been designed with extreme >>> flexibility in mind, together with Sebastien's work you may find it >>> easier to incorporate your Matlab -> Python converted functions into >>> relax. Seb might even have some opinions on the subject ;) >>> >>> Also, because of the relax design, it should be possible to copy the >>> Python functions directly into NESSY and the whack the GUI into shape >>> to use them without modification. However NESSY would probably >>> require major heart surgery to get minfx into it to allow the R1rho >>> data type to be used, which you may be required to perform. >>> >>> If you do decide to go with either NESSY or relax, could I ask you to >>> communicate on the public mailing lists? Cheers. Also, for the >>> Matlab script and other files, I would open a special task for you in >>> either project where files can be attached (note that attaching files >>> to the task tracker is permanent - they can never be deleted). I >>> would also recommend that you sign up with Gna! and then we can set >>> you up as a developer of either (or both) projects and create a branch >>> that you can play with. For NESSY you would automatically be a >>> developer, but for relax I would give you restricted access to just >>> your branch, and then later on the relax developers can vote to have >>> you as a full developer. >>> >>> Regards, >>> >>> Edward >>> >>> >>> P. S. Note that I would be helping you in my spare time - i.e. after >>> work and on weekends, so you may sometimes have to wait for a >>> response. Especially if I needed to help you with the coding. >>> >>> >> >> -- >> Sébastien Morin, Ph.D. >> 1183 Bursins, Switzerland >> ---- sebastianomorino AT gmail.com ---- >> _______________________________________________ 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
