Conversion of Bruker processed data to CSDM

[rsarkar281]

Dear Developers,
I would like to fit an experimental Bruker MAS spectrum. In doing so, I would like to import the Topspin processed spectrum into the CSDM format. This is because if I process the data using nmrglue and similar methods shown (https://mrsimulator.readthedocs.io/en/stable/introduction/fitting_example.html#import-experimental-dataset) , I have a very bad baseline, and subsequently the fit results are not satisfactory. The problem is if I convert the bruker processed data using nmrglue.bruker.read_pdata and then convert this to CSDM, it doesn't find the proper ppm scale. Could you please let me know how to do this ? Many thanks,

[deepanshs]

Hi,

Thanks for reaching out. We are aware of this issue and are working with nmrglue to fix the issue. The fix pr in nmrglue -> jjhelmus/nmrglue#227

It might be a while till the next version of nmrglue with the fix releases. I am attaching a script with you to read the process data using nmrglue. Let me know if you have any other questions.

Testing_MRsimulator_csdmpy.ipynb.zip

Best,
Deepansh

[BiffoQ]

Hi @BiffoQ, could you share the Bruker data from your example? My guess is that the error with different shapes is related to how the bruker data is converted to csdm. I can look into more if you share the file.

Best, Deepansh

yes, you are right.

the count or size of independent variable x of processed and unprocessed Bruker's data, in this case, are not the same. because i am using the processed data for simulation and storing the dimension of the unprocessed data in the spectral dimensions variable, thus the error.

kindly find the NMR data attached.

8.zip

[BiffoQ]

I have been able to resolve the error but I am having problems with the fitting now.

I have played with constraining both the isotropic chemical shift and eta, but nothing seems to be working.

Can you kindly help with that?

I have attached the code, and the data is the same as the 8.zip file.

51V_fitting.zip

Thank you for your swift response.

[BiffoQ]

So, I tried the code with other data, and the 1st order CQ fit works perfectly with reasonably optimised parameter values and errors.

The initial data looks good to me, and I am confounded about why the fitting won't work- maybe some unexplained phenomenon or something. It would be nice to unravel that. On second thoughts, it could be that CQ might not be the dominant nuclei perturbation; maybe CSA might also be playing a role.

see attached the fitting script and data that worked.

Script:
51V_fitting_working_new_spectrum.zip

Data:
1.zip

I would also like to fit a Czjzek model to this data, but I am hitting a bottleneck. I would greatly appreciate it if you could help with this. Should I drop the problem under this discussion?

Thank you for your time.

[deepanshs]

Hi @BiffoQ ,

For the 8.zip data, the issue was with bruker to csdm conversion via nmrglue. I have updated the function in nmrglue with the fix. The attached notebook contains the updated function with fix and the remaining code works as expected.
51V_fitting_fix.ipynb.zip

For the 1.zip dataset, the scipt looks fine to me. The slight discrepancy in the fit could be from multiple factors unrelated to the code.

Have to looked at the czjzek and extended czjzek examples on the doc. It might be a good starting point.
https://mrsimulator.readthedocs.io/en/stable/fitting/1D_fitting/plot_7_27Al_Extended_Czjzek.html#sphx-glr-fitting-1d-fitting-plot-7-27al-extended-czjzek-py

Best,
Deepansh

[BiffoQ]

Hi @deepanshs,

Thanks for the fix. The updated function works perfectly well, and I can confirm that I have been able to fit my data.

Regarding the Czjzek and extended Czjzek, I have been able to implement the 27Al example on my data; however, the problem arises while trying to adapt the 139La example. I think I am satisfied with what I have achieved so far.

Thanks once again.

Cheers,

Abdulkadir.