Protein backbone assignment

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Joefred Kyei

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Sep 6, 2026, 11:44:43 PM (3 days ago) Sep 6
to NMR POKY/SPARKY USER GROUP

Hi,

I assigned my experimental 1H–15N HSQC peaks using BMRB reference chemical shifts. In the peak list, the reference resonance shift and the experimental peak shift appear as separate rows.

Is there a way to display the reference chemical shift and the corresponding experimental peak chemical shift side-by-side?

Thank you.

Screenshot 2026-09-06 234143.png

Lee, Woonghee

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Sep 6, 2026, 11:52:10 PM (3 days ago) Sep 6
to Joefred Kyei, NMR POKY/SPARKY USER GROUP

Hi,

 

The easiest way is to go to your BMRB entry page. At the very bottom of the page, you should find a link labeled “SPARKY: Backbone.” Open that file in SPARKY, and you should be able to view the reference and experimental chemical shifts together.

 

 

Best,

 

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

 

Associate Professor & Data Science and Chemistry Certificate Program Director

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

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

 

Shipping/Mailing Address:

Woonghee Lee

1201 5th St. UCD CHEM-194

P.O. Box 173364 (USPS)

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From: nmr-s...@googlegroups.com <nmr-s...@googlegroups.com> on behalf of Joefred Kyei <joefre...@gmail.com>
Date: Sunday, September 6, 2026 at 9:45 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] Protein backbone assignment

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Joefred Kyei

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Sep 7, 2026, 9:50:16 AM (3 days ago) Sep 7
to Lee, Woonghee, NMR POKY/SPARKY USER GROUP
Thank you. I imported the BMRB reference directly into POKY using the BMRB entry number. I can see both the reference and experimental shifts, but they are mixed together in the peak list. Is there a way to distinguish the reference shifts from the experimental shifts?  

Lee, Woonghee

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Sep 7, 2026, 9:55:07 AM (3 days ago) Sep 7
to Joefred Kyei, NMR POKY/SPARKY USER GROUP
In that case, I would suggest this way.

  1. "bs" : Simulate N-HSQC using BMRB
  2. "ct" : Contour color change
  3. "eo": Overlay


Woonghee Lee, I.E.I.P., M.S., Ph.D.
 
Associate Professor & Data Science and Chemistry Certificate Program Director
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
 
 
Shipping/Mailing Address:
Woonghee Lee
1201 5th St. UCD CHEM-194
P.O. Box 173364 (USPS)
Denver, CO 80204, USA
Sent: Monday, 07 September 2026 07:49:30
To: Lee, Woonghee <WOONGH...@ucdenver.edu>
Cc: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Protein backbone assignment
 

Joefred Kyei

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Sep 7, 2026, 10:03:54 AM (3 days ago) Sep 7
to Lee, Woonghee, NMR POKY/SPARKY USER GROUP

Hello Dr. Lee,

Thank you. I can already see both the BMRB resonance shifts and my experimental peak shifts in the peak list, but they are mixed together. I was wondering if there is a way to display them side by side, like “resonance vs. peak,” so I can compare the shifts more easily.

Could you please take a look at the picture I sent earlier? It shows how they are currently displayed.

Lee, Woonghee

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Sep 7, 2026, 10:10:51 AM (3 days ago) Sep 7
to Joefred Kyei, NMR POKY/SPARKY USER GROUP
That is what I am suggesting.
Once you create a simulated spectrum using “bs,” the new spectrum will contain the assigned reference peaks. You can then simply use “lt” to open a new peak list window that shows only the reference peaks.
This way, you can have two peak list windows side-by-side: one for the reference peaks and one for your experimental peaks. You do not need to keep the reference peaks in your actual experimental spectrum.

Woonghee Lee, I.E.I.P., M.S., Ph.D.
 
Associate Professor & Data Science and Chemistry Certificate Program Director
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
 
 
Shipping/Mailing Address:
Woonghee Lee
1201 5th St. UCD CHEM-194
P.O. Box 173364 (USPS)
Denver, CO 80204, USA

From: Joefred Kyei <joefre...@gmail.com>
Sent: Monday, September 7, 2026 8:03:56 AM

To: Lee, Woonghee <WOONGH...@ucdenver.edu>
Cc: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Protein backbone assignment
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