 |
 |
Dear Martin, If you are going to do anything more than the NOE ratio I would suggest using relax. http://www.nmr-relax.com/ This has the advantage that it calculates errors from RMSD values within Sparky, and if peaks are near the water line for example, you can change the RMSD value for that individual peak so that it would have a larger error. If you do choose to do this, it's fairly laborious but the results that come out are quite good and are then ready to input into Lipari-Szabo model free calculations using 'relax' along with T1 and T2 values (which relax can also calculate from peak heights, though you should make sure they're all picked correctly by using Analysis to check curve fitting first) if that is what you want to do. The program can also tell you if your results are consistent between two different fields (consistency.py script). In addition the manual is absolutely excellent and has a lot of the theory and technical details within it. This is how you do it. 1. Export peak lists from Analysis in Sparky format (making sure the order is 1. heteronucleus, 2. proton - you'll see what I mean when you do this). 2. You need to be able to open your spectra in Sparky, so > pipe2ucsf hsqc.ft2 hsqc.ucsf should process them to the correct format. 4. Open in sparky by typing 'fo' into the box, zoom out so you can see the whole spectrum (zo) and select a typical region of the spectrum with no peaks (rm - then drag the mouse over where you want). At this point you can also get RMSD values for any peaks that are in regions with a lot of noise. 5. Using the 'noe.py' script within relax you should be able then get the values (noe.out) and Grace graphs. 6. You can either run relax using the command line eg. '> relax noe.py' or by using the GUI (though I personally find it more useful to use the command line). Hope this helps, Madeleine Strickland MCJC Group N317, School of Chemistry, Bristol University On Tue, April 17, 2012 12:03 am, CCPNMR automatic digest system wrote: > There are 3 messages totaling 183 lines in this issue. > > Topics of the day: > > 1. Calculation of HetNOE measurements > 2. Calculation of HetNOE errors (2) > > ---------------------------------------------------------------------- > > Date: Mon, 16 Apr 2012 12:12:19 +0200 > From: Martin Ballaschk <[log in to unmask]> > Subject: Calculation of HetNOE measurements > > Dear all, > > I'm using the Data Analysis -> Heteronuclear NOE feature of Analysis 2.1.5 > and so far it was working quite well for me. > > Now I encountered a dataset where the reported SD is nearly zero. I > suppose that's not the way is should be. > I'm at a loss at this point: I have no idea how the error calculation in > CCPN actually works. > > How is the error actually calculated? Is Analysis determining the S/N > ratio? > > Is there a way to change the calculation parameters or somehow influence > the error determination procedure? > > Cheers > Martin > > > -- > Martin Ballaschk > AG Schmieder > Leibniz-Institut für Molekulare Pharmakologie > Robert-Rössle-Str. 10 > 13125 Berlin > Tel.: +49-30-94793-234/315 > Büro: A 1.26 > Labor: C 1.10 > > ------------------------------ > > Date: Mon, 16 Apr 2012 17:22:02 +0200 > From: Martin Ballaschk <[log in to unmask]> > Subject: Re: Calculation of HetNOE errors > > Dear all, > > most likely my problems with the small error values are coming from the > bad quality of the spectrum. > > But anyway, if anyone knows how CCPN calculates the HetNOE errors, I'd > appreciate if she could share the knowledge. I tried to dig through the > CCPN documentation but couldn't find any information about this. > > Cheers > Martin > > -- > Martin Ballaschk > AG Schmieder > Leibniz-Institut für Molekulare Pharmakologie > Robert-Rössle-Str. 10 > 13125 Berlin > [log in to unmask] > Tel.: +49-30-94793-234/315 > Büro: A 1.26 > Labor: C 1.10 > > ------------------------------ > > Date: Mon, 16 Apr 2012 17:39:54 +0200 > From: Melanie Schwarten <[log in to unmask]> > Subject: Re: Calculation of HetNOE errors > > > Hi, > > there is an old message on the mailing list, describing how the errors > are calculated in Analysis. > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0905&L=CCPNMR&P=R3497&1=CCPNMR&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0905&L=CCPNMR&P=R3497&1=CCPNMR&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4> > > As it is based on the noise levels bad quality (does this mean low > signal to noise ratio?) should yield in big errors. > > Cheers, > Melanie > > > On 04/16/2012 05:22 PM, Martin Ballaschk wrote: >> Dear all, >> >> most likely my problems with the small error values are coming from the >> bad quality of the spectrum. >> >> But anyway, if anyone knows how CCPN calculates the HetNOE errors, I'd >> appreciate if she could share the knowledge. I tried to dig through the >> CCPN documentation but couldn't find any information about this. >> >> Cheers >> Martin >> >> > > > -- > Dr. Melanie Schwarten > Institut de Biologie Structurale J.P. Ebel > Laboratoire de Résonance Magnétique Nucléaire (LRMN) > 41, rue Jules Horowitz > F-38027 GRENOBLE Cedex 1 > > ------------------------------ > > End of CCPNMR Digest - 13 Apr 2012 to 16 Apr 2012 (#2012-53) > ************************************************************ > Madeleine Strickland MCJC Group N317, School of Chemistry, Bristol University