Hi Edward The developer is Peter Neidig. I can contact him and ask him to change to rates instead of times. Do you want me to write him a mail with cc to you or the list?
Cheers Michael Am 20.10.2010 09:32, schrieb Edward d'Auvergne: > Hi, > > On 19 October 2010 23:40, Michael Bieri<[email protected]> wrote: > >> Hi Edward >> ... >> >> Am 19.10.2010 22:46, schrieb Edward d'Auvergne: >> >>> Hi Micheal, >>> >>> I've had a look at the PDC files, and there are 2 issues we need to >>> deal with (that I can see for now). Firstly Bruker is reporting T1s >>> and T2s. That in itself is not a problem as it is easy to convert to >>> R1 and R2 - an essential step in using the data. The problem is with >>> the errors, you can't simply invert them! There is no way to convert >>> these T1 and T2 errors into R1 and R2 errors that I know of. So I >>> would suggest that we need to recalculate the R1 and R2 and obtain the >>> errors by Monte Carlo simulations. This can be done easily as the PDC >>> files contain all that is needed. Maybe we need to talk to Bruker >>> about this. >>> >>> >> I think the problem with the errors of T2 / R2 can be converted by >> adding the error and subtracting the error to the mean value, invert >> them and get the new error. >> > This works for linear relationships, but this is hyperbolic as you are > performing an inversion. Therefore there is no direct mapping of the > normal distribution equation of T2 errors to the normal distribution > of R2 errors. I think we really need to talk to Bruker so they might > reconsider this choice! None of the model-free programs - relax, > modelfree, dasha, or tensor - can use T1 and T2 values. That is > because Abragam's original equations are in terms of rates, and the > natural process is a rate. We should point the Bruker developers > behind the Bruker Dynamics Centre to these emails. This is very > important, T1 and T2 errors are totally useless to the field. They > can't even be used for spectral density mapping, SRLS, or anything! > Bruker is making a very silly mistake here!!! Do you know who the > person in charge is? Is Wolfgang involved? > > > >>> The second is, how does Bruker calculate the errors? We will have to >>> ask them. For a data analysis, errors are just as important, or maybe >>> even more important than the data itself. So they need to be properly >>> estimated using the gold standard of Monte Carlo simulations - without >>> question. For the R1s and R2s, the errors is obviously come from the >>> duplicated spectra. But for the NOEs, it is totally unclear where the >>> errors come from. For the NOE, the error can be directly calculated - >>> no MC sims required - but where do they get their estimate of the >>> base-plane noise? We really need to be certain where the NOE errors >>> in the PDC file come from. >>> >>> >> According to Bruker, the error originates from duplications and noise of >> the spectra. In addition, they included a function, where the user can >> specify the error themselves.... >> > This sounds ok. Will have to give the software a try to see if they > can improve on their error estimates. These errors are incredibly > important, so this really needs to be done right. > > > >> Probably it makes sense to import the Bruker files and generate relax >> parameter files. What do you think about this? I suggest to save those >> files and the user will further analyse these data. In case of the GUI, >> the files are placed in the model-free section. >> > If Bruker fixes the time vs. rate error problem, then all we need to > do is to modify relax_data.read() and read the R1, R2, and NOE > directly from the PDC files. Otherwise we are in trouble and will > have to perform the R1 and R2 exponential fitting again. We could > bootstrap the T1 errors to R2 errors, but it would be easier to > re-perform the curve-fitting. As for the GUI, this could be just part > of loading the relaxation data files. If it is implemented in the > back end through relax_data.read(), as soon as the system test passes, > the GUI will also be fully able to use the PDC files. > > If we can get rates in the PDC files, then reading peak intensities is > not needed. Users could do this anyway by removing all extra lines > from the PDC file and using sprectrum.read_intensities() as it > currently is. This would be useful to validate the performance of the > Bruker software. > > Regards, > > Edward > > > >> Cheers >> Michael >> >> >>> Regards, >>> >>> Edward >>> >>> >>> >>> >>> On 7 October 2010 07:35, Michael Bieri<[email protected]> >>> wrote: >>> >>> >>>> URL: >>>> <http://gna.org/task/?7180> >>>> >>>> Summary: Import of BRUKER Protein Dynamic Center Protject >>>> Project: relax >>>> Submitted by: michaelbieri >>>> Submitted on: Donnerstag 07.10.2010 um 16:35 >>>> Should Start On: Donnerstag 07.10.2010 um 00:00 >>>> Should be Finished on: Donnerstag 07.10.2010 um 00:00 >>>> Category: relax's source code >>>> Priority: 1 - Later >>>> Status: In Progress >>>> Privacy: Public >>>> Percent Complete: 0% >>>> Assigned to: michaelbieri >>>> Open/Closed: Open >>>> Discussion Lock: Any >>>> Effort: 0.00 >>>> >>>> _______________________________________________________ >>>> >>>> Details: >>>> >>>> BRUKER is developing a Protein Dynamic Center (PDC). This program will have >>>> an interface with relax, so data collected with TopSpin and NOE, T1 and T2 >>>> values calculated by PDC can be imported into relax and analyzed. >>>> >>>> An import function has to be created for the prompt and GUI interface. In >>>> addition, the PDC manual has to be corrected (see attachment chapter 8). >>>> >>>> The manual, T1, T2 and NOE sample data are attached. >>>> >>>> >>>> >>>> _______________________________________________________ >>>> >>>> File Attachments: >>>> >>>> >>>> ------------------------------------------------------- >>>> Date: Donnerstag 07.10.2010 um 16:35 Name: testT1.txt Size: 23kB By: >>>> michaelbieri >>>> >>>> <http://gna.org/task/download.php?file_id=10640> >>>> ------------------------------------------------------- >>>> Date: Donnerstag 07.10.2010 um 16:35 Name: testT2.txt Size: 23kB By: >>>> michaelbieri >>>> >>>> <http://gna.org/task/download.php?file_id=10641> >>>> ------------------------------------------------------- >>>> Date: Donnerstag 07.10.2010 um 16:35 Name: testNOE.txt Size: 8kB By: >>>> michaelbieri >>>> >>>> <http://gna.org/task/download.php?file_id=10642> >>>> >>>> _______________________________________________________ >>>> >>>> Reply to this item at: >>>> >>>> <http://gna.org/task/?7180> >>>> >>>> _______________________________________________ >>>> Nachricht geschickt von/durch Gna! >>>> http://gna.org/ >>>> >>>> >>>> _______________________________________________ >>>> relax (http://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://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://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
