Hi, If you didn't have the temperature compensation (with either single-scan interleaving or temperature compensation blocks), then I would highly recommend you use Sebastien Morin's relaxation data consistency testing analysis built into relax. This will say if there are problems with the data. If this is the case, then any Rex values you obtain should be ignored as it is likely to be fake (see the Tjandra 96 paper about this).
For the diffusion tensor, I think in the Morin and Gagné paper you link to (http://dx.doi.org/10.1016/j.bpj.2009.02.068), a special script was written for this. Sebastien might be able to say a bit more about this. The way you would do this is to write a custom script which reads in the final relax results file you would like to use, use the fix user function to un-fix the diffusion tensor while fixing all the model-free parameters, run 500 Monte Carlo simulations, and the save the result. This shouldn't be too hard to write, though you might need to read the user function documentation. Regards, Edward On 24 May 2012 10:18, Romel Bobby <[email protected]> wrote: > Hi Edward, > > I have data at two field strengths with proper temperature calibration. > Unfortunately, by the time I ran the experiment we didn't have proper > temperature compensation included for the T2 experiment. However, I ran the > T2 experiment with alternating delays per t1 increment, so that the average > CPMG delay was kept more or less constant. > > I used the dauvergne_protocol.py to do the S2 analysis and afterwards ran > the final_data_extraction.py script to extract the model-free parameters. > > My question regarding the error for the diffusion tensor components and for > the global correlation time was in respect with a paper I read > (doi: 10.1016/j.bpj.2009.02.068). They have used relax and reported > errors.I'm inclined to do the same and could use some advice how to go about > it the correct way. > > Kind regards, > > Romel > > > > On Friday, 11 May 2012, Edward d'Auvergne <[email protected]> wrote: >> Dear Romel, >> >> Welcome to the relax mailing lists! To be able to answer your >> question, would you be able to give more details about your analysis? >> Which scripts did you use, i.e. did you use the dauvergne_protocol.py >> script? And if not, would you be able to describe how you implemented >> the full, highly iterative analysis (see my response to Fernando >> Amador, http://www.mail-archive.com/[email protected]/msg01158.html), >> possibly attaching your hand written scripts. And do you have data at >> two or three field strengths, all with proper temperature compensation >> and per-experiment temperature calibration? >> >> As for the extraction of diffusion tensor errors, this will not be >> possible with the implementation of the dauvergne_protocol.py script. >> You can see the analysis implementation details in the >> auto_analyses/dauvergne_protocol.py file, specifically in the >> execute() method on line 525. If you go down to the part titled >> 'Final run', you will see that just at the start of the Monte Carlo >> simulation section that the diffusion tensor is fixed prior to the >> simulations. The reason for this is that the diffusion tensor is the >> biggest contributor to the relaxation data. Hence if it is allowed to >> move, this has a large affect on the model-free parameters. Although >> it shouldn't change your model-free parameter errors too much (this >> has never been investigated by the NMR field to date, as far as I >> know), the result is that each simulation takes an incredibly long >> time to complete. Instead of optimising many models of 1-6 >> parameters, this will optimise the global model of all model-free >> parameters of all models simultaneously with the diffusion tensor >> parameters, i.e. a single model of hundreds to thousands of >> parameters. If you would like to perform Monte Carlo simulations on >> such a global model, you will require either a few years computation >> time or access to a cluster and then look into Gary Thompson's >> multi-processor implementation for relax. >> >> I hope this info helps, >> >> Regards, >> >> Edward >> >> >> >> On 11 May 2012 06:35, Romel Bobby <[email protected]> wrote: >>> Hi all, >>> >>> First of all, I want to thank the users and developers on this mailing >>> list >>> for their constant support for people like me. This forum has helped me >>> with >>> several issues. >>> >>> Recently, I have started using relax to extract model-free parameters >>> from >>> NMR spin relaxation experiments and so far I've been happy with the >>> software. >>> For my analysis, I've been using the model scripts that come with the >>> software and at the end, after optimisation and model selections, I've >>> been >>> extracting the results from the final run, ie after the MC simulation, by >>> using the script written by Michael Bieri >>> >>> However, that script gives me the final values for the rotational >>> correlation time and parameters for the diffusion tensor among many >>> other. >>> However, from the script one cannot get the errors associated with the >>> correlation time (and also for the diffusion tensor parameters). Surely, >>> from the MC simulations it ought to be possible to get an estimation on >>> the >>> uncertainties of these values (?). >>> Unfortunately, I'm not very familiar with the interior of relax, or >>> python >>> for that matter, that I was able to find a solution yet. >>> >>> Any kind of help/suggestion will be greatly appreciated. >>> >>> Kind regards, >>> >>> Romel Bobby, PhD Student >>> Biomolecular NMR Research Group >>> School of Chemical Sciences/School of Biological Sciences >>> The University of Auckland >>> +64 (09) 3737599 Ext 83157 >>> >>> _______________________________________________ >>> relax (http://www.nmr-relax.com) >>> >>> This is the relax-users 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-users >>> >> > > -- > Romel Bobby > > Biomolecular NMR Research Group > School of Chemical Sciences/School of Biological Sciences > The University of Auckland > +64 (09) 3737599 Ext 83157 _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users 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-users
