MNova to POKY

[Chris Lee]

Hello,

I am a complete beginner with POKY. Is there a way to import MestReNova (MNova) spectra into POKY? If not, how about a way to import the raw FID datafile?

Thanks for any help,

Chris

[Lee, Woonghee]

Dear Chris,

 

There are a few ways. 

 

1. Mnova -> UCSF
1. Save as .csv from Mnova.
2. Use csv2ucsf.py (http://pine.nmrfam.wisc.edu/download_scripts.html)
2. TopSpin 2rr -> UCSF

1. Just drop “2rr” into POKY main window.
2. Using NMRPipe -> UCSF

1. Just drop “.dat”/”.ft2” into POKY main window. 

 

Hope this helps.

 

 

Best,

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A (office), Rm 4128 (dry lab), Rm 4133 (wet lab)

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

From: <nmr-s...@googlegroups.com> on behalf of Chris Lee <chris...@gmail.com>
Date: Friday, May 13, 2022 at 11:29 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] MNova to POKY

 

[External Email - Use Caution]Hello,

 

I am a complete beginner with POKY. Is there a way to import MestReNova (MNova) spectra into POKY? If not, how about a way to import the raw FID datafile?

 

Thanks for any help,

Chris

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[Chris Lee]

Hi Dr. Lee,

I have tried using the csv2ucsf.py script, but am running into an issue where the chemical shift ranges displayed on the x and y-axis of POKY are incorrect. I suspect it has something to do with me not providing the optional arguments "-o1" and "-o2" with csv2ucsf.py, but I'm not sure what to put there. The script mentions that "-o1" is "position of matrix index 0 in ppm for axis 1" and "-o2" is "position of matrix index 0 in ppm for axis 2"; however, I am not sure what "matrix index 0" is referring to. Could you perhaps take a look at the .csv file (attached) and offer any thoughts?

Also another thing: when I load the converted .ucsf file into POKY, the spectrum seems to be rotated 180 degrees relative to what is seen in MNova. Do you have any thoughts on why this might be the case as well?

Thank you,

Chris

[Lee, Woonghee]

Dear Chris,

 

Those oN parameters are the very downfield ppms (the lowest ones).   

 

Also another thing: when I load the converted .ucsf file into POKY, the spectrum seems to be rotated 180 degrees relative to what is seen in MNova. Do you have any thoughts on why this might be the case as well?

 

Isn’t that something mnova saves incorrectly?

 

Best,

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A (office), Rm 4128 (dry lab), Rm 4133 (wet lab)

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

From: <nmr-s...@googlegroups.com> on behalf of Chris Lee <chris...@gmail.com>

Date: Monday, May 16, 2022 at 2:55 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>

Subject: Re: [NMR POKY/SPARKY] MNova to POKY

 

[External Email - Use Caution]Hi Dr. Lee,

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/a8d26d5a-b473-47bd-ba9b-8f31dc3439d3n%40googlegroups.com.

[Chris Lee]

Hi Dr. Lee,

Regarding the rotated spectrum, I've confirmed that MNova saves the correct peak intensity values at the correct chemical shifts when exporting to the CSV. So I think the issue must be with either the conversion script or the way POKY reads in the converted .ucsf file. 

I could send you the MNova file, CSV file, my command line options for the conversion script, and the output ucsf if you'd like, but it looks like the file sizes are too big to attach to this message. Could I perhaps send a drive link to your UC Denver email address?

Thank you,

Chris

[Lee, Woonghee]

Dear Chris,

 

CSV is just the format for comma-separated values. You can just transpose like this web page.

https://stackoverflow.com/questions/4869189/how-to-transpose-a-dataset-in-a-csv-file

 

You can either do that on pythonshell (py) or use Poky Notepad.

 

Best,

Woonghee

 

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/fe05fde9-8d2f-4a39-8a81-1b4c6e3a83fcn%40googlegroups.com.

[Chris Lee]

Hi Dr. Lee,

Thank you for the suggestion; however, transposing is not the issue. Transposing the input data file simply flips the spectrum about the diagonal; however, the problem I'm facing is that the spectrum in POKY is actually rotated about the center point - i.e, the signals are displayed at the wrong chemical shift coordinates.

For example, if I have a 2D spectrum that's 10 ppm by 10 ppm in size from 0 to 10 ppm along both axes, a signal that should be present in the upper right quadrant at say 2.0 ppm along f2 and 1.0 ppm along f1 (and which is present at those coordinates in the .csv file exported from MNova), would now be displayed in POKY at 8.0 ppm along f2 and 9.0 ppm along f1 after the conversion to the .ucsf file.

Regards,

Chris

[Lee, Woonghee]

Dear Chris,

 

Once it is csv, you can do whatever you want. There are tons of information out there. For instance, https://blender.stackexchange.com/questions/142024/moving-and-rotating-using-csv

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/7766ab84-89e0-48c3-9aa3-21b75f5dc8abn%40googlegroups.com.