Hi, I'm now back from holidays. Please see below:
On 28 October 2010 23:51, Michael Bieri <[email protected]> wrote: > Hi Edward > > I was in contact with Bruker about the conversion of the errors of T1/T2 > to R1/R2. I was not aware of the 'Propagation of Uncertainty'. > > He was recalculating his fits of T1/T2 for R1/R2 and compared the > errors. They were exact for 5 decimal places. This should be accurate enough. A percentage error would be nicer to have though. Though I don't understand why they want or need T1/T2 times and not relaxation rates, as all the fundamental NMR theory uses rates. It would be horrible if half the protein NMR people started publishing graphs in papers of Tx values rather than Rx, while the rest continue with Rx values!!! This would be an absolute nightmare. > So we could simply calculate the error of R1/R2 as follows: > > Rx = 1/Tx > errRx = R * errTx/T Did Peter give this equation? This seems a little strange as R/T = R^2, so then errRx = R^2*errTx or errRx = errTx/T^2. Would you know if there is an error in this equation? Is there a reference for this equation? > This should be simple to implement! If the equations are correct, we should be able to read the rates and errors in directly with the relax_data.read() user function, and then perform model-free analysis as normal. For the next version of the GUI, maybe we can implement the relax_data.read() user function as wizard type GUI element where: 1) ri_label, frq_label, and frq are first given. 2) The file is then selected. This would perform the automatic file type detection. 3) The *_col and sep args can then be supplied for the generically columnar formatted input files (a bit like the Excel CSV file import dialog). This would be skipped for PDC or other specially formatted files. For non-GUI related operation, Bruker have the option of controlling relax automatically. Though I don't know if they would be interested in this as it would require installing Python, all the necessary python modules, bmrblib (https://gna.org/projects/bmrblib/), minfx (http://gna.org/projects/minfx/), and relax. Although this could be bundled all together and be part of the Protein Dynamic Center without the users having to do any work. If we implement the PDC file handling, they could provide the model-free related GUI elements needed (i.e. something similar to your GUI) and use the automatic protocol (http://www.nmr-relax.com/refs.html under "The new model-free analysis protocol"). I don't know how Bruker would like the idea of the 1-2 weeks computation time required for a complete high precision model-free analysis. The GUI would also remove some of the flexibility currently in relax for having multiple diffusion tensors, or parts of the molecule having local_tm parameters while other parts have a common diffusion tensor. But they have the option of further integration of relax and PDC via this path, and could in the end have the full model-free results within the PDC and even have the ability to submit results to the BMRB. From our point of view though, this is not ideal as users might forget that relax is doing all the work behind the scenes and we may not get citations. And it would duplicate and make redundant your GUI currently going into relax. Regards, Edward P.S. Maybe you could forward this message to Peter and the other Bruker people behind the PDC? It would be good to get them involved in these discussions. Cheers. > > Cheers > Michael > > 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. >> >> 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. >> >> 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
