Dictionary


Written by: Piotr Klukowski
Published: Jan. 12, 2022, 6:02 p.m.




Axes disambiguation
This property specifies the order of axes in the uploaded spectrum file. Its possible values are stored in "Project Summary" as multiple choice list, such as the one presented in the figure below.

Each option in the list presents a possible mapping of axes specific to the selected experiment type (e.g. 13C-HSQC) to dimensions in the uploaded spectrum. Options printed in green are more likely to be correct than the red options. Each option contains a list of axes in the following format:
A: B (C, D MHz, E ppm)
A - axis name in the Cyana library (specific to the selected spectrum type)
B - axis ID (ω1, ω2, ...)
C - axis name extracted from the header of the uploaded spectrum file
D - axis range in MHz extracted from the header of the uploaded spectrum file
E - chemical shift range in ppm extracted from the header of the uploaded spectrum file

A common mistake is to wrongly disambiguate 1H axes in 3D/4D NOESY and HCCH-TOCSY experiments. Some difficulties in spectrum disambiguation might be resolved by inspecting spectrum visualizations available in "Project Summary → Info", and comparing them with the examples presented in the table below.

Spectrum typeAxis labelsExample visualizations
13C-resolved [1H-1H] NOESYC
HC - hydrogen covalently bonded to C
H - hydrogen interacting through-space with HC-C
HC-H, HC-C, H-C
15N-resolved [1H-1H] NOESYN
HN - hydrogen covalently bonded to N
H - hydrogen interacting through-space with HN-N
HN-H, HN-N, H-N
CCH-TOCSYC1 - carbon 1
C2 - carbon 2
H1 - hydrogen covalently bonded to C1
C2-C1, H1-C1, H1-C2
HBHAcoNHN
HN - hydrogen covalently bonded to N
H
HN-H, HN-N, H-N
HCCH-TOCSY / HCCH-COSYC
HC - hydrogen covalently bonded to C
H
H-HC, HC-C, H-C
HCcoNHN
HN - hydrogen covalently bonded to N
H
HN-H, HN-N, H-N
15N-TOCSYN
HN - hydrogen covalently bonded to N
H
H-N, HN-N, H-HN




Spectrum unfolding
This property specifies the ID of the axis with folded/aliased signal. If aliased signals have opposite amplitude to regular (unaliased) signals, one can limit the scope of the automated unaliasing procedure to positive or negative signals only.
For example in 13C-resolved [1H, 1H]–NOESY it is common to fold signals along 13C dimension. Assuming that 13C correspond to the second dimension in the uploaded spectrum, option ω2 should be selected.

Spectrum tags
It is possible to provide additional information about the uploaded spectrum using a subset of predefined tags:

TagDescription
@ALIonly signals from aliphatic atoms have been recorded
@AROonly signals from aromatic atoms have been recorded
@NEGanalyze only signals with negative signal amplitude
@POSanalyze only signals with positive signal amplitude
wA:Bshift spectrum along axis A by B ppm (e.g w1:0.4)

All tags associated with a spectrum can be provided in the "Project Summary" as comma-separated values. For example, signals in a spectrum with the tags:
@ALI,w1:0.4
will be shifted along the 1st axis by 0.4 ppm and assigned only to aliphatic atoms.

Spectra name convention and supported data formats
NMRtist uses Sparky (*.ucsf) format to store and process NMR data. Spectra uploaded in other formats are converted automatically to Sparky format during the upload process, as presented in the table below.

FormatRequired file extensionDescription
SparkyucsfNMRtist native format, no conversion required
NMR pipepipeFile is automatically converted using the pipe2ucsf tool available in Sparky/bin directory
BrukerzipBruker spectra are uploaded as single zip file, which contains the full Bruker directory tree of the spectrum. Processed spectrum data (i.e. 2rr or 3rrr) must be available in the pdata subdirectory. The uploaded zip file is automatically extracted and converted using the bruk2ucsf tool available in Sparky/bin directory. An example zip file with a Bruker spectrum can be downloaded here.
XEASYzipSpectra in XEASY format are uploaded as single zip file, which contains 2 files (*.3D.16, *.3D.param). The uploaded zip file is automatically extracted and converted using Yokochi converters. An example zip file with a XEASY spectrum can be downloaded from here.

In case of problems with automated online conversion, it is recommended to convert spectra to Sparky format locally and then proceed with the upload.

If the filename of an uploaded spectrum matches the pattern
spectrumType_spectrumTags

for example
C13NOESY_@ALI@NEG

then the spectrum type and tags are set automatically in the "Project Summary". Only @ALI, @ARO, @POS and @NEG tags are allowed in the filename.

Application call status
StatusDescriptionAllowed user actions
WaitingApplication call request has been registered in the NMRtist system. Waiting for computational resources.OpenCancelRemove
RunningApplication is currently running on NMRtist computational node (or computer cluster)OpenCancelRemove
FinishedApplication results have been fetched from NMRtist computational node (or computer cluster)OpenCancelRemove


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