Follow-up Comment #12, sr #2336 (project relax):
hanks 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
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.
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.
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 am having trouble looking at these. When I type those help commands, I
get the error (Traceback (most recent call last):
File "<console>", line 1, in <module>
NameError: name 'spectrum' is not defined)
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?
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.
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[sr #2336] xpk files