Hi Catherine,
You may try SSnake (
https://gitlab.science.ru.nl/mrrc/nmrzoo/ssnake).
Although is made for solid-state NMR, it can process 2D NMR data very
easily (I already used for HSQC/HMBC).
Best,
----------------
Dr. Igor d'Anciães Almeida Silva
Research Scientist - NMR Core
University of Missouri-Columbia
32A Chemistry Building
________________________________
> From: main_at_ammrl.groups.io on behalf of Catherine Deborde via groups.io
> Sent: Monday, November 4, 2024 6:48 AM
> To: main_at_ammrl.groups.io
> Subject: [AMMRL] Need help for JRES processing
Hi Ammrl colleagues,
A colleague of mine, in charge of the NMR processing workflow of a large
project where NMR is using for food metabolomics, is having issues understanding
how a JRES spectrum is processed, and in particular what is behind the
TopSpin xfb command.
Has any attempted to replicate in python language what the xfb command does
and been successful ? My colleague doesn't want to reinvent the wheel if
someone has done this.
See below the details about his questions.
Any help you can provide would be useful.
Thanks!
Catherine Deborde
INRAE
NMR Lab leader, BIBS Facility (Bioressources : Imaging, Biochemistry, Structure)
3 rue Yvette Cauchois, La Géraudière CS 71627
44 300 Nantes, France
NMRProcFlow: http://www.nmrprocflow.org/
MOOC métabolomique: http://www.dailymotion.com/video/x6mt32w
NMR in action for ANR CaDON: https://www.youtube.com/watch?v=F3vSDFviHSM
***************************************************************************
In details:
After running the xfb command, he found the following line in the pdata/1/auditp.txt file:
xfb F2: SI = 8K WDW = 3 SSB = 0 FT_mod = 6 PKNL = 1
F1: SI = 128 WDW = 3 SSB = 0 FT_mod = 6 FCOR = 0.5 PH_mod = 2
From the TopSpin reference doc:
WDW = 3 SSB : window multiplication mode - qsine : Squared Sine Bell- SSB=0
FT_mod = 6 : Fourier transform mode / F2: AQ_mod = 3, F1: FnMODE = 0 => forward, quad, complex
PKNL = 1 : group delay compensation - causes a non linear 5th order phase correction of the raw data.
FCOR = 0.5 : first (FID) data point multiplication factor - on 2D Avance data in the second direction
PH_mod = 2 : phase correction mode - Magnitude calculation
PH_mod=2 (mc) involves a phase correction in the F1 dimension using the
magnitude calculation. What does this mean from an algorithmic point of view?
Does it means that the spectra matrix in the F1 dimension is replaced by
its corresponding magnitude matrix ?
The complete processing seems to me to be as follows:
1 - process the direct dimension (F2)
a) sine-squared apodization (WDW = 3 SSB = 0)
b) zero-filling (x2)
c) FFT (AQ_mod = 3 => forward, quad, complex)
d) group delay compensation (PKNL = 1)
2 - process the indirect dimension (F1)
a) transposition of the spectra matrix
b) first (FID) data point multiplication factor (FCOR = 0.5)
c) sine-squared apodization (WDW = 3 SSB = 0)
d) zero-padding
e) zero-filling (x2)
f) FFT (FnMODE= 0 => forward, quad, complex)
g) phase correction mode - Magnitude calculation (PH_mod = 2 => mc)
h) transposition of the spectra matrix
He is trying to reproduce the same processing as the xfb command using a py=
thon script using nmrglue, but he can't do it. Maybe he missed or misunders=
tood one or more steps? Thanks for your help.
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Received on Mon Nov 04 2024 - 06:19:59 MST