On Wed, 26 Jun 2019 at 10:02, Yulian Gavrilov <[email protected]> wrote: > Thank you. > Actually I used CCPN analysis ands saved my data in Sparky format. > In CCPN I used simple box sum method. This should be compatible with error > propagation, right?
Ah, that's different then ;) Note that you cannot use their "truncated box sum" method. So have a look at https://www.nmr-relax.com/manual/spectrum_integration_points.html. If N is different for each peak, it might require some manual work to get all the information in. Why do you save in Sparky format? Is there a CCPN output format with the volumes and the number of points in the box? If so, we might be able to add relax support for such input data and automate the process. > However, there is another problem. I don't see the way to get base plane > noise rmsd from CCPN. > I wonder if I can use Sparky for example, only to get rmsd of the base plane > noise and CCPN only to get the volume of the peaks. This is more difficult due to the scaling/truncation some softwares perform. You could cross check that the peak height is 100% identical in both - and only then can you combine the data. But does the "box sum" method in CCPN only report the sum, or does it include a standard deviation? I suggest contacting the CCPN people to explain the problem and to ask them if there is a way to measure the RMSD of the baseplane noise within a user-defined box. Note that, due to spectral processing and spectral artefacts, different regions of the NMR spectra have different RMSDs. In a HSQC, the chopped out side of spectra, right of the water signal, almost always has a lower RMSD than around your peaks. From my own personal experience, contributing factors include a baseplane roll (of the noise, not the average) due to truncation of strong peaks, noise due to impurities in the NMR sample, proximity to the water signal, proximity to the edge of the spectrum, and window function choice. So a whole spectrum RMSD measurement is quite useless for a relaxation analysis. Regards, Edward _______________________________________________ nmr-relax-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/nmr-relax-users
