Exporting/Importing .nef files for CYANA calculations

Hi Eliza @ElizaP
I am having some difficulties with compatibility between v3 and getting CYANA to read and write .nef files. As far as I can tell, CYANA can read .nef files but gets stuck on recognising the dimensions of 1H-1H NOESY spectra (copied below). Do you have any tips on how I need to edit my .nef files to get CYANA to read them?
Thanks,
Anne


cyana> read nef CX0001_CCPproj1.nef
*** WARNING: Unsupported NEF format version `1.0`.
*** ERROR: Cannot read line 277 in frame `nef_nmr_spectrum_CX0001_NOESY_pH6_298K`:
           1  ppm  1H  700.4732885  9.99724  9.775281268  circular  true  .  H1
    NMR exchange format file `CX0001_CCPproj1.nef` read.

Hi Anne,

Cyana (cyana-3.98.13 version) needed few changes in NEF file to read it. All spectra information that are written in NEF file need to agree with cyana-3.98.13/lib/cyana.lib file.

In your exported NEF file:

1. In the saveframe for your spectra (for instance: save_nef_nmr_spectrum_2dnoe`1`) you should change _nef_nmr_spectrum.experiment_type tag to use Cyana nomenclature from cyana.lib file.
For 2d NOESY it should be:
_nef_nmr_spectrum.experiment_type NOESY

2. In the `_nef_spectrum_dimension` _loop _nef_spectrum_dimension.axis_code also have to be changed (again in accordance with cyana.lib).
It should look like this:
loop_
_nef_spectrum_dimension.dimension_id
_nef_spectrum_dimension.axis_unit
_nef_spectrum_dimension.axis_code
_nef_spectrum_dimension.spectrometer_frequency
_nef_spectrum_dimension.spectral_width
_nef_spectrum_dimension.value_first_point
_nef_spectrum_dimension.folding
_nef_spectrum_dimension.absolute_peak_positions
_nef_spectrum_dimension.is_acquisition

1 ppm H1 749.7835083 16.67147898 13.12757051 circular true .
2 ppm H2 749.7835083 13.33718319 11.46041975 circular true .
stop_

3. To avoid NEF version warning you should change:
_nef_nmr_meta_data.format_version 0.91
This tag is the first saveframe (save_nef_nmr_meta_data)

Hopefully this should help.

If you have any questions please let me know.
Eliza

(02-03-2021, 12:24 pm)ElizaP Wrote: Hi Anne,

Cyana (cyana-3.98.13 version) needed few changes in NEF file to read it. All spectra information that are written in NEF file need to agree with cyana-3.98.13/lib/cyana.lib file.

In your exported NEF file:

1. In the saveframe for your spectra (for instance:    save_nef_nmr_spectrum_2dnoe`1`) you should change _nef_nmr_spectrum.experiment_type tag to use Cyana nomenclature from cyana.lib file.
For 2d NOESY it should be:
_nef_nmr_spectrum.experiment_type  NOESY

2. In the `_nef_spectrum_dimension` _loop _nef_spectrum_dimension.axis_code also have to be changed (again in accordance with cyana.lib).
It should look like this:
     loop_
        _nef_spectrum_dimension.dimension_id
        _nef_spectrum_dimension.axis_unit
        _nef_spectrum_dimension.axis_code
        _nef_spectrum_dimension.spectrometer_frequency
        _nef_spectrum_dimension.spectral_width
        _nef_spectrum_dimension.value_first_point
        _nef_spectrum_dimension.folding
        _nef_spectrum_dimension.absolute_peak_positions
        _nef_spectrum_dimension.is_acquisition

        1  ppm  H1  749.7835083  16.67147898  13.12757051  circular  true  .
        2  ppm  H2  749.7835083  13.33718319  11.46041975  circular  true  .
     stop_

3. To avoid NEF version warning you should change:
_nef_nmr_meta_data.format_version   0.91
This tag is the first saveframe (save_nef_nmr_meta_data)

Hopefully this should help.

If you have any questions please let me know.
Eliza
Thanks Eliza!
This solved my problem and I can now write .prot and .peaks files from my .nef file.