Re: Displaying Cyana assignment in Poky

Abhishek Bastiray

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Sep 24, 2026, 2:37:05 PM (11 days ago) Sep 24

to NMR POKY/SPARKY USER GROUP

Dear Prof. Lee,

I am trying to import XEASY/CYANA peak list files (.peaks) for my - and -edited NOESY spectra into Poky. Although Poky successfully reads the files and the peaks appear in the spectra, the CYANA assignments are not displayed.

Could you please advise me on what I may be missing and how I can import or configure the peak lists so that the assignments are visible in Poky?

Thank you very much for your time and assistance.

Regards,

Abhishek

Lee, Woonghee

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Sep 24, 2026, 2:39:14 PM (11 days ago) Sep 24

to Abhishek Bastiray, NMR POKY/SPARKY USER GROUP

Hi,

Are you using “cy”, or something else?

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

Associate Professor & Data Science and Chemistry Certificate Program Director

Department of Chemistry

Center for Advanced Computational Molecular Science

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

https://clas.ucdenver.edu/chemistry/data-science-and-chemistry-certificate

Shipping/Mailing Address:

Woonghee Lee

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Denver, CO 80204, USA

From: 'Abhishek Bastiray' via NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Date: Thursday, September 24, 2026 at 12:37 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] Re: Displaying Cyana assignment in Poky

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Abhishek Bastiray

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Sep 24, 2026, 2:49:23 PM (11 days ago) Sep 24

to NMR POKY/SPARKY USER GROUP

Yes I am using 'cy' to load the data but poky does not display the assignment.

Lee, Woonghee

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Sep 24, 2026, 3:15:51 PM (11 days ago) Sep 24

to Abhishek Bastiray, NMR POKY/SPARKY USER GROUP

“cy” looks correct. It seems assignments in .peaks are not recognized correctly.

Please check if those corresponding highlighted columns in your .peaks are not zeros.

1 126.912 7.956 7.953 1 U 2.11e+07 0 e 0 0 0 0 0

2 111.835 7.442 7.442 1 U 9e+06 0 e 0 0 0 0 0

3 111.830 6.735 7.442 1 U 6.48e+06 0 e 0 0 0 0 0

Just in case, I just made a new POKY Notepad script that you can find from POKY Notepad -> Files -> POKY Scripts -> Find Additional … or “Commands” button in the main window.

Search for “cyana2pokylist.py” and ctrl/cmd+b. You will be able to generate .list file that you can load using “rp”. If the generated file does not have assignments but only ?-?-?, then your file format isn’t recognizable.

Best,

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Abhishek Bastiray

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Sep 24, 2026, 3:50:51 PM (11 days ago) Sep 24

to NMR POKY/SPARKY USER GROUP

The Notepad script seem to work but when I try to just convert the N15.peaks (output from Cyana) using the .prot file as input, I also see some C13 assignment (presumbly from the 13C NOESY assignment). I am not sure where those data are being introduced from.

Thank you,

Abhishek

Lee, Woonghee

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Sep 24, 2026, 3:52:43 PM (11 days ago) Sep 24

to Abhishek Bastiray, NMR POKY/SPARKY USER GROUP

My concern is that assignment numbers in your .peaks inconsistent with your .seq file used here. Because the assignment number in the .peaks refers to first column in .seq.

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