Issue loading in peaks from an NEF file from CCPNMR 3.0.4

[Rodrigo Muzquiz]

Hi Woonghee,

I was trying to load in my chemical shift list and assignments from a project in CCPNMR to poky, however, whenever I try to read the file using 'rp' only a few lines are read. The rest of the lines in the file including the atoms, chemical shifts, and sequence identifiers were listed as unreadable lines. I used an NEF file that was exported from CCPNMR. I loaded in the same spectra that were used in CCPNMR into poky after converting the files to .ucsf. Is there an easier way to transfer assignments between CCPNMR projects and poky?

Thank you,

Rodrigo Muzquiz 

[Lee, Woonghee]

Dear Rodrigo,

 

“rp” reads POKY/SPARKY format peak list. Not NEF. NEF was discussed among software developers and the meetings have not been resumed since the covid19 outbreak. I would say NMR-STAR 3.1/3.2 is accepted format at least for my development. I don’t know CCPNMR can generate it. You can find some options from Poky -> Universal NMR formats. Once you generate POKY/SPARKY resonance list file, you can simply read that in in Resonances tab, then use “ta” to populate assigned peaks in spectra.

 

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

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> on behalf of Rodrigo Muzquiz <muzquiz...@gmail.com>
Date: Wednesday, July 20, 2022 at 1:20 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] Issue loading in peaks from an NEF file from CCPNMR 3.0.4

 

[External Email - Use Caution]Hi Woonghee,

 

I was trying to load in my chemical shift list and assignments from a project in CCPNMR to poky, however, whenever I try to read the file using 'rp' only a few lines are read. The rest of the lines in the file including the atoms, chemical shifts, and sequence identifiers were listed as unreadable lines. I used an NEF file that was exported from CCPNMR. I loaded in the same spectra that were used in CCPNMR into poky after converting the files to .ucsf. Is there an easier way to transfer assignments between CCPNMR projects and poky?

 

Thank you,

 

Rodrigo Muzquiz 

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[Rodrigo Muzquiz]

I see, thank you! I was able to load in the chemical shift list into the resonance list tab. For the transfer assignments command is there a way to select solid-state experiments? The list only shows solutions experiments to transfer to. I am specifically looking for NCACX and NCOCX. 

From,

Rodrigo 

[Lee, Woonghee]

Sure. PAG tab -> Protein NMR (MAS solid-state) -> #11 “TA”

 

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

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> on behalf of Rodrigo Muzquiz <muzquiz...@gmail.com>

Date: Wednesday, July 20, 2022 at 2:13 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>

Subject: Re: [NMR POKY/SPARKY] Issue loading in peaks from an NEF file from CCPNMR 3.0.4

 

[External Email - Use Caution]I see, thank you! I was able to load in the chemical shift list into the resonance list tab. For the transfer assignments command is there a way to select solid-state experiments? The list only shows solutions experiments to transfer to. I am specifically looking for NCACX and NCOCX. 

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/15cda1fa-675f-4e77-a940-790545208f22n%40googlegroups.com.