sparky to BMRB NMRSTAR conversion

[Adedolapo Ojoawo]

Hi Woonghee,

I am trying to use the ARECA tool to validate my assignments using NOE peaks, but I need to generate a BMRB NMRSTAR file. Is there a POKY module available for conversion of the POKY assignment list to BMRB NMRSTAR v3.1 or 2.1 for chemical shift validation? I tried looking through POKY for this but couldn't find so I thought I should ask.

Thanks

Adedolapo

[Lee, Woonghee]

Dear Adedolapo,

 

Have you checked Poky menu -> Universal NMR Formats?

 

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 <nmr-s...@googlegroups.com> on behalf of Adedolapo Ojoawo <amoj...@gmail.com>
Date: Tuesday, April 25, 2023 at 2:34 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] sparky to BMRB NMRSTAR conversion

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[Adedolapo Ojoawo]

Yes, I saw the format in that menu but this is not a script, right? It only shows the format for each file type which I already have. I was just wondering if there is a POKY script implemented for the conversion from sparky/poky assignment format to BMRB NMRSTAR format. So that I don't have to go through the whole reformatting using Excel (unless there's actually an easy way of doing this that I don't know about)

Adedolapo

[Lee, Woonghee]

 

I think you don’t need to use Excel. You can just import poky/sparky resonance list file generated from “rl” window in the resonances tab. Then, use “es” to generate NMR-STAR 3.1 will do the job I believe.

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/f20df1fa-2b76-4085-999a-8bace5cefbe6n%40googlegroups.com.

[Adedolapo Ojoawo]

Thanks, Woonghee! The "es" command worked fine. 

Adedolapo

[stefano ciurli]

Hello,

 

I am trying to test the POKY structure builder on a PC with Ubuntu. After having loaded the sequence and the assignment of the scalar-coupled spectra, as well as having aligned the 3D N- and C-NOESY spectra, when I try to load them in the window “NMR thru-space data, I get the message: “Error Selected thru-space file file is invalid”.

 

What is the problem?

Thanks a lot!

Stefano

[Lee, Woonghee]

Dear Stefano,

 

It means the file is not understandable by Poky Structure Builder. If you cannot fix it, you can just use “Import” button and select the experiment instead.

 

 

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 (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: stefano ciurli <stefano...@gmail.com>
Date: Wednesday, May 3, 2023 at 9:05 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>, Lee, Woonghee <WOONGH...@UCDENVER.EDU>
Subject: PONDEROSA with POKY Builder

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Hello,

[stefano ciurli]

Dear Woonghee,

 

what you are suggesting is exactly what I am doing. I click on the button defined as “Import thru-space peaks from current Poky”

The importing of the two 3D NOESYs works instead if I manually open the .ucsf file.

 

However, the program crushes repeatedly with the message “Aborted (core dumped).

I checked the peak lists generated by AUDANA/AUDASA and only the peaks in the N-NOESY are found.

 

Help is needed, thanks!

 

Stefano

[Lee, Woonghee]

Dear Stefano,

Can you make peak lists from "lt" with data heights turned on, and use open button not import? If it still complains, can you share the peak list file with me privately?

Thanks,

Woonghee

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From: nmr-s...@googlegroups.com <nmr-s...@googlegroups.com> on behalf of stefano ciurli <stefano...@gmail.com>
Sent: Thursday, May 4, 2023 2:25:32 AM
To: Lee, Woonghee <WOONGH...@UCDENVER.EDU>; NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] Re: PONDEROSA with POKY Builder

 

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