Re: I-Pine question

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

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Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

From: Buchko, Garry W <Garry....@pnnl.gov>
Date: Sunday, December 15, 2024 at 11:34 PM
To: Lee, Woonghee <WOONGH...@UCDENVER.EDU>
Subject: I-Pine question

[External Email - Use Caution]

Hi Lee,

Sorry to bother you again and perhaps this is a question you don’t have an answer for.

I started using NMRtist a few months ago and was mostly pleased with how well it assisted assignments. While I long knew it was there, I decided to try I-PINE associated with Poky. I was astonished….it maybe did a better job! One question.

I tested it on a ~ 50 kDa, dimeric protein (25 kDa monomer) that is triple labelled, 2H, 13C, 15N. I collected a C-beta optimized HNCACB experiment on the sample and many more b-carbon cross peaks appeared. With NMRtist, I can enter both HNCACB data sets (B-optimized and normal) and the assignments are much better with both (I didn’t try C-beta alone) . With I-PINE, it looks like I can only add one HNCACB data set. Is there a way to feed it both HNCACBs? (I’ve not yet tried to see if just adding the B-optimized HNCACB is good enough (there is an HNCA, HNCOCA, and gcbcaconh…..)).

Best,

Garry.

From: Lee, Woonghee <WOONGH...@UCDENVER.EDU>
Date: Wednesday, January 24, 2024 at 7:09 AM
To: Buchko, Garry W <Garry....@pnnl.gov>
Subject: Re: Bruker to USCF conversion with Poky Ventura

2rr alone isn't enough. It doesn't have necessary meta information. acqu*, proc* files in the parent-parent folder are needed.

Woonghee

--

Woonghee Lee, Ph.D.

Assistant Professor of Chemistry

University of Colorado Denver

https://groups.google.com/g/nmr-sparky

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Lee, Woonghee

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Dec 16, 2024, 1:21:04 PM12/16/24

to Buchko, Garry W, NMR SPARKY USER GROUP, pinenmr-u...@googlegroups.com

Dear Garry,

User groups are here:

https://groups.google.com/g/pinenmr-user-group

It is still okay to ask me since mostly I answer.

For the NOESY, I-PINE only sees peak patterns not intensities. Even it does not assign directly NOE peaks. Only uses peak pattern similarities in different strips. Also, please note that only 15N-NOESY is used during the assignment. 13C-NOESY is used in the full automation mode that goes through 3D structure calculations. In case resonance assignments are successful and both 15N and 13C NOESY are provided, PONDEROSA-C/S will be automatically tried to get you 3D structures. Hope this helps.

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

Assistant 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

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

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

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

From: Buchko, Garry W <Garry....@pnnl.gov>
Date: Monday, December 16, 2024 at 11:12 AM
To: Lee, Woonghee <WOONGH...@UCDENVER.EDU>
Cc: NMR SPARKY USER GROUP <nmr-s...@googlegroups.com>, pinenmr-u...@googlegroups.com <pinenmr-u...@googlegroups.com>
Subject: Re: I-Pine question

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Super, thanks. I was thinking about “a” but wasn’t sure if this was possible. I thought I tried “b” but the program didn’t like something (it was in an early attempt and perhaps I did something else wrong). I’ll both try again.

I’ll also look for the mailing list (and avoid troubling you so much).

For a peak-picked NOESY data set, do you know if I-pine makes use of the cross peak intensities? In a triple labelled sample (grown in just D2O) the side chain signals are significantly weaker (many non-exsistent) than for the exchangeable protons.

Thank you again and cheers,

Garry.

From: Lee, Woonghee <WOONGH...@UCDENVER.EDU>
Date: Monday, December 16, 2024 at 7:27 

AM

To: Buchko, Garry W <Garry....@pnnl.gov>

Cc: NMR SPARKY USER GROUP <nmr-s...@googlegroups.com>, pinenmr-u...@googlegroups.com <pinenmr-u...@googlegroups.com>
Subject: Re: I-Pine question

Check twice before you click! This email originated from outside PNNL.

Lee, Woonghee

unread,

Aug 21, 2025, 1:16:04 PMAug 21

to Buchko, Garry W, NMR SPARKY USER GROUP, pinenmr-u...@googlegroups.com

Dear Garry,

The “Pre-assignment” option still requires your data to align with your given assignments. If there’s some strong dominating pair over your given assignment, that kind of thing can happen still. If you can make an assignment in 3D, that will definitely help by rebalancing expected carbon chemical shifts, however that is not mandatory most cases.

One thing greatly improves the results is that, for example, if you don’t see a peak in HNCACB that is expected (you see in HNCA, CBCACONH…), place that in HNCACB even though you don’t see it in there. Simply copy and paste from one to the HNCACB.

For the CO pair, it is less strong potential energy term than CA/CB pairs due to the nature of the experiment. But if your CA/CB experiment is inferior, you can assign it on HNCO/HNCACO to improve the effect of “Pre-assignment”.

Hope this helps.

Best,

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

Assistant 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