Subject: Re: how sparky deal with 1H-15N relaxation data?
From: andrewjamesperry2002
Date: Apr 4, 2006

Previous: 102

To add to Joshs comments ..

shameless plug

Some new software for relaxation dynamics analysis, by Edward
dAuvergne, has recently come to maturity (it has been in development
for ~5 years). It fixes several problems with the commonly used
methodology, and produces more reliable results than can be calculated
with Modelfree program. relax is designed to do all the analysis
from relaxation curve fitting, diffusion tensor fitting, and fitting
model-free dynamics parameters. It takes Sparky peak lists (among
other formats) as input, and so may be a good option for the type of
analysis you are doing.

http://www.nmr-relax.com/

/shameless plug

The relax manual explains a method for error calculation for the NOE
( http://www.nmr-relax.com/manual/node31.html ), with the relevant
equations. It is a good idea to use the Sparky rm function to get
the RMSD of the spectrum as a maximal noise estimate in several areas
free of peaks. If there are peaks which may be in noisier regions (eg
near the water line) it can be a good idea to give those peaks
seperate errors by measuring the RMSD near those peaks seperately.

You can get more detail on how relax calculates R1 and R2 errors in
the manual also, and by typing:

help(relax_fit.mean_and_error)

at the relax prompt.

More in depth questions about this would probably best be answered on
the relax mailing list ( https://mail.gna.org/listinfo/relax-users/ ).

Hope this helps,

Andrew

--- In nmr_sparky@yahoogroups.com , jleeweir jleeweir@... wrote:

hi,everyone:

Now Im working on dynamics of protein and have many questions!

First,sparky can deal with T1,T2 with a seris of 2D spectra and get
error without duplicating several experiments.How sparky do that? Is
the error of R1 or R2 equal wih T1 and T2?

Second,I dont konw how to deal with noe via sparky? How to get its
error?

Thanks to all!