Dear Elio, Sorry for the delay. I hadn't realised that there were unanswered questions here. Please see below for more comments.
On Fri, May 29, 2009 at 3:14 PM, Elio Cino <[email protected]> wrote: > Thanks for the reply. > > > 1) Which program are you using to measure peak intensities? >> nmrviewj > >> 2) For peak intensities, are you using heights or volumes? >> intensities from nmrviewj The intensity just is the amount of signal, and can be the height at the top of the peak, the volume of part or all of the peak, or some other measure. This is important for the error analysis part. >> 3) How exactly are you getting your noise estimates? >> RMSD of the >> entire spectrum? RMSD of a box over the peak? Or >> RMSD of the region >> between peaks? > I think this only applies for the NOE. I am using a box between peaks, and > getval in nmrviewj to get the Sdev (usually around 0.018 for my NOE data). I > just put this value into the noe.py script. Does anyone know how getval works? Does it give an RMSD? A SSE? A chi-squared? Is it the integral of absolute values? >> 4) Are you using the same program for peak intensities and peak >> errors? If not, this is fatal - absolute values change >> wildly between >> different programs and spectrum formats. Hence why S/N >> ratios are >> important. >> Yes, I use nmrviewj for both. > >> 5) You mentioned you have duplicates. Could you >> elaborate? Do you >> have 10 spectra for the R1 experiment and 2 of these are in duplicate? >> For the NOE, are these in duplicate or triplicate (note >> that single >> spectra are all that are necessary)? > For T1, and T1rho, I have 12 spectra each, and 2 from each are duplicates > (10 novel spectra for each T1 and T1rho). >> >> 6) You said that spectrum.read_intensities() with NMRView >> worked in >> the end, but this is impossible with relax-1.3.3. Have you >> checkedout a copy of the 1.3 repository line with this new code? > >> Hmm... maybe I was not clear. I didn't know how to get nmrview lists read >> (relax was looking for sparky), and was asking how to do this. I was getting >> some strange responses for some reason, but eventually found out all I had >> to do was include "format='nmrview' into the relax_fit.py script where I >> load in the xpk files. This allowed relax to run successfully. I am using >> 1.3.3 on linux. I have not made any other changes to the sample relax_fit.py >> script besides adding the format='nmrview' part. Ok, rudimentary NMRView support is in relax-1.3.3. I can't remember exactly, but I think the support has significant problems. This should be fixed in the 1.3 line, where format detection is now automatic. >> 7) If you are using the 1.3 repository line code, have you >> carefullyread the documentation for all the 'spectrum' user >> functions? E.g: >> relax> help(spectrum.baseplane_rmsd) >> relax> help(spectrum.error_analysis) >> relax> help(spectrum.integration_points) >> relax> help(spectrum.read_intensities) >> relax> help(spectrum.replicated) > >> I looked over some of the briefly. Am I supposed to be doing anything else >> other than running the sample script with my xpk files in order to >> successfully get relaxation rates for my data? The script should be modified to suit your system, but other than that it should be the same. >> 8) Could you attach your relax script to your email? >> And maybe the >> input and output data for a single spin system where you see a >> difference between the matlab script and relax? > > > I am not currently at my workplace. I can get the script later, and some > differences later. But, it is just the sample script provided with 1.3.3 > with my xpk files being loaded. The same goes for the noe.py script (I also > put in the noise sdev value from nmrview for this one). The T1, T1rho rates, > and NOE all have fairly high errors when processed with relax compared to my > other method. I would like to use relax, but need to figure out why it is > giving such high errors. Many of the T1 rates have errors 150+% in relax for > some reason. I am only using well-resolved peaks. Maybe there > is something small I am missing..any help is appreciated. Is this now working? In all of my test data, I have not seen this error. Oh, do you mean T1 or R1? If you invert the R1 value to get T1 and then invert the sigma_R1 value to get the sigma_T1 standard deviation, this is a mistake that would cause errors > 100%. To find the exact problem (assuming it still exists and is really a problem), creating a bug report would be very useful. This process is described in detail in the manual. Attaching files containing one or two lines of data which reproduce the problem would be extremely useful for me to be able to track down the problem. A full description of the other programs and values obtained would also be very useful. Cheers, Edward _______________________________________________ relax (http://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
