Hi Seb, The details are mainly for the archived records, as this is going to the development list (http://thread.gmane.org/gmane.science.nmr.relax.devel/3790/focus=3826). It will be useful for reference. Thank you again for the relaxation dispersion branch. Even though you didn't manage to complete it, your code has made it extremely easy for me to get this analysis up and running.
Cheers, Edward On 11 April 2013 22:30, Sébastien Morin <[email protected]> wrote: > Hi Ed, > Hi all, > > Thanks for you messages, especially for the second message sparing my > effort. > > Would you have any other question, please feel free to ask... > > Just as an update, I am no longer in active research (although I will always > be happy to help research, if I can) since I joined the International AIDS > Society (based in Geneva) as the Research Officer for the Industry Liaison > Forum (www.iasociety.org/ilf.aspx). > > Best of the best for your research around protein dynamics ! > > Sincerely, > > > Seb :) > > > > > On 13-04-11 5:09 PM, Edward d'Auvergne wrote: >> >> 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 was too out of date), 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 ---- >>>> > > -- > 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
