Hi
Essentially XFB does the following on each dimension
1. Window function
2. Zero fill
3. Fourier transform
4. Phase correct
Possibly with the addition of bells and whistles like linear prediction and
water suppression by convolution [there are lots of flags]
There is another thing you have to allow for the jres spectra: they have a
45 degree tilt which has to be removed…
This is done via the tilt command you may also want to to symmetrise with symj
An example of processing is in the au macro folder in proc_jres as a macro
And there is a good paper on jres here
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/epdf/10.1002/pca.1186
For a much more nuts and bolts approach to nmr data processing I would have
a look at nmrpipe, topspin is quite prescriptive in the way it expects you
to process spectra…
Nmrpipe: https://www.ibbr.umd.edu/nmrpipe/install.html
Hope that helps
regards
Gary
Dr Gary S Thompson NMR Facility Manager
CCPN CoI & Working Group Member
Wellcome Trust Biomolecular NMR Facility
School of Biosciences, Division of Natural Sciences
University of Kent, Canterbury, Kent, England, CT2 7NZ
☎:01227 82 7117
✉️: g.s.thompson_at_kent.ac.uk
orchid: orcid.org/0000-0001-9399-7636
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Thanks Igor,
I forward your message to my colleague.
He will check the github and try ssSNAKE.
I'll keep you updated.
Thanks again,
Catherine
> De : main_at_ammrl.groups.io De la part de D'Anciaes Almeida Silva, Igor
> Envoyé : lundi 4 novembre 2024 15:20
> À : main_at_ammrl.groups.io
> Objet : Re: [AMMRL] Need help for JRES processing
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, Stru=
cture)
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 python
script using nmrglue, but he can't do it. Maybe he missed or misunderstood one
or more steps? Thanks for your help.
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