Can assign with TOCSY also get distance limit data like "UPL"?

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Sooho Ko

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Jun 26, 2025, 12:44:55 PMJun 26
to NMR POKY/SPARKY USER GROUP
Dear all,

I got structure on Poky Structure Builder, but This is the result obtained by replacing the unnatural amino acid with ALA. So I need the UPL file to analyze the structure again in CYANA.

I assigned NOSEY and TOCSY 1H-1H peaks. But when i get upl file from "gd", there was only from NOESY spectrum.

Also, there is only data between different amino acids in the upl file, and there is no data within one amino acid (ex A1 HA-H).

Is there any way to get more detailed distance data?


Best regards,
 Sooho Ko

Lee, Woonghee

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Jun 26, 2025, 6:30:57 PMJun 26
to Sooho Ko, NMR POKY/SPARKY USER GROUP
TOCSY is through bond experiment. You can't get distance restraints. 

"xf" is another plugin you can create both tbl and upl. Distance should be put it in by yourself based on intensity.

Intra Distance from intensity is often inaccurate though due to variety of reasons. So "gd" excludes them by default.  

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

Shipping/Mailing Address:
Woonghee Lee
1201 5th St. UCD CHEM-194
P.O. Box 173364 (USPS)
Denver, CO 80204, USA
From: nmr-s...@googlegroups.com <nmr-s...@googlegroups.com> on behalf of Sooho Ko <gosu...@gmail.com>
Sent: Thursday, June 26, 2025 10:14:55 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] Can assign with TOCSY also get distance limit data like "UPL"?
 
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Sooho Ko

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Jun 26, 2025, 11:12:16 PMJun 26
to NMR POKY/SPARKY USER GROUP

I understand, thank you.

Lastly, is there a way to get a .peaks file for run cyana? I'm going to do an analysis using the .peaks file and .prot file.

I don't know if I used Pokebuilder incorrectly, but the peaks file I got from builder

# Number of dimensions 2
#FORMAT xeasy2D
#INAME 1 H
#INAME 2 h
#CYANAFORMAT Hh
1 1.472 1.470 1 U 6.55e+07 0.000E+00 a 0 0 0
2 1.436 1.433 1 U 6e+07 0.000E+00 a 0 0 0
3 1.528 1.529 1 U 4.57e+07 0.000E+00 a 0 0 0
......

It comes out as unsigned data as above. And when use CYANA with proton list and this data, following upl comes out empty.

Thank you.
2025년 6월 27일 금요일 오전 7시 30분 57초 UTC+9에 Lee, Woonghee님이 작성:

Lee, Woonghee

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Jun 27, 2025, 12:00:41 AMJun 27
to Sooho Ko, NMR POKY/SPARKY USER GROUP
To make peaks and prot, try "xe". AUDANA generates .prot and .peaks file for the user's cyana run, but does not assign .peaks file. Only .list files. If you only need files to run cyana, just xe will do. The format you have attached seems fine to me.

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

Shipping/Mailing Address:
Woonghee Lee
1201 5th St. UCD CHEM-194
P.O. Box 173364 (USPS)
Denver, CO 80204, USA
Sent: Friday, June 27, 2025 8:42:26 AM

To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Can assign with TOCSY also get distance limit data like "UPL"?

Sooho Ko

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Jun 28, 2025, 9:21:48 AMJun 28
to NMR POKY/SPARKY USER GROUP
I have made a lot of progress thanks to you. I hope you have a great weekend!

Thank you!


Sooho Ko

2025년 6월 27일 금요일 오후 1시 0분 41초 UTC+9에 Lee, Woonghee님이 작성:
To make peaks and prot, try "xe". AUDANA generates .prot and .peaks file for the user's cyana run, but does not assign .peaks file. Only .list files. If you only need files to run cyana, just xe will do. The format you have attached seems fine to me.

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

Shipping/Mailing Address:
Woonghee Lee
1201 5th St. UCD CHEM-194
P.O. Box 173364 (USPS)
Denver, CO 80204, USA
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