NMRtist

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 type	Axis labels	Example visualizations
¹³C-resolved [¹H-¹H] NOESY	C HC - hydrogen covalently bonded to C H - hydrogen interacting through-space with HC-C	HC-H, HC-C, H-C
¹⁵N-resolved [¹H-¹H] NOESY	N HN - hydrogen covalently bonded to N H - hydrogen interacting through-space with HN-N	HN-H, HN-N, H-N
CCH-TOCSY	C1 - carbon 1 C2 - carbon 2 H1 - hydrogen covalently bonded to C1	C2-C1, H1-C1, H1-C2
HBHAcoNH	N HN - hydrogen covalently bonded to N H	HN-H, HN-N, H-N
HCCH-TOCSY / HCCH-COSY	C HC - hydrogen covalently bonded to C H	H-HC, HC-C, H-C
HCcoNH	N HN - hydrogen covalently bonded to N H	HN-H, HN-N, H-N
¹⁵N-TOCSY	N 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:

Tag	Description
@ALI	only signals from aliphatic atoms have been recorded
@ARO	only signals from aromatic atoms have been recorded
@NEG	analyze only signals with negative signal amplitude
@POS	analyze only signals with positive signal amplitude
wA:B	shift 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 1^st 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.

Format	Required file extension	Description
Sparky	ucsf	NMRtist native format, no conversion required
NMR pipe	pipe	File is automatically converted using the `pipe2ucsf` tool available in Sparky/bin directory
Bruker	zip	Bruker 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.
XEASY	zip	Spectra 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.

Other data file formats
Starting from 27.03.2023, in addition to NMR spectra, NMRtist supports the following file formats: (a) manual peak lists (*.list, *.peaks), (b) chemical shift lists (*.prot), (c) chemical shift statistics (*.stats), (c) lower/upper distance restraints (*.lol/*.upl), (d) Talos angle restraints (*.aco), and (e) protein structure (*.pdb). These files can be uploaded to the project storage and used as inputs for the applications. The table below contains example files in formats compatible with NMRtist.

File type	Format	Example files	Comment
Manual peak list	XEASY (.peaks), Sparky (.list)	N15HSQC (Sparky, unassigned) N15HSQC (Sparky, assigned) N15NOESY (Sparky, unassigned) N15NOESY (Sparky, assigned) N15HSQC (XEASY, unassigned) N15HSQC (XEASY, assigned) N15NOESY (XEASY, unassigned) N15NOESY (XEASY, assigned)	In the uploaded peak list, you may specify both assigned and unassigned peaks. Please note that NMRtist disregards any peak assignments, allowing you to manually add them to your project using *.prot files. For all application types, you can utilize manual peak lists as input data.
Chemical shift lists	CYANA (*.prot)	Download	The chemical shift list, which serves as input for the application, fixes the chemical shifts to the specified values in the uploaded file. The application accepts both complete and partial chemical shift lists, accommodating various data availability.
Chemical shift statistics	CYANA (*.stats)	Download	The chemical shift statistics file functions similarly to the chemical shift list file (.prot) but applies softer constraints. Instead of fixing the chemical shift to predefined values (.prot), NMRtist prioritizes the shifts specified in the .stat file, assigning them only when feasible. Each specified chemical shift in the stats file must have a non-zero "tolerance" value. This tolerance helps the method identify favorable regions in the spectra where the chemical shift is anticipated. Chemical shift statistics files are useful for chemical shift transfer applications. In this scenario, the target protein spectra are uploaded to the project, while the homolog protein chemical shifts are stored in a .stat file.
Lower/upper limit restraints	CYANA (.lol, .upl)	Download	During the CYANA structure calculation step, specified restraints are employed alongside the restraints extracted from NMR spectra to enhance the accuracy of the resulting model.
TALOS angle restraints	TALOS (*.aco)	Download	In the ARTINA workflow, specified restraints take the place of the TALOS step. The uploaded aco file will be used directly during the structure calculation phase.
Protein structure	PDB (*.pdb)	Download	Protein Structure Model (AlphaFold prediction, X-ray, or homolog structure): Enhances the accuracy of chemical shift assignment (if the uploaded model is within <3Å backbone RMSD of the measured protein) Can be utilized for structure-based assignment. Remark I: We recommend using structure files solely for chemical shift assignment. For structure determination, the structure file can serve as input; however, the results will be heavily biased towards the input structure. Remark II: Uploading protein bundles is preferable to single-model PDB files (e.g., X-ray). AlphaFold typically generates five structure proposals. While it is possible to use a single (best) proposal as input, we advise creating a PDB file containing all five models before uploading it to NMRtist projects.

The files stored in the above table are compatible with the following protein sequence:
MKIISISETPNHNTMKITLSESREGMTSDTYTKVDDSQPAFINDILKVEGVKSIFHVMDFISVDKENDANWETVLPKVEAVFELEHHHHHH

Application call status

Status	Description	Allowed user actions
Waiting	Application call request has been registered in the NMRtist system. Waiting for computational resources.	Open Cancel Remove
Running	Application is currently running on NMRtist computational node (or computer cluster)	Open Cancel Remove
Finished	Application results have been fetched from NMRtist computational node (or computer cluster)	Open Cancel Remove