Load your own NMReDATA zipfile:
If local, it must be in the same folder.
Load sample files:
Small files for quick testing:
File contents
(click on items to display them if feasible)
Save edited file
To save the package:
to an NMReDATA file.
To add a file to the existing NMReDATA package:
The file will be added inside this folder:
and
choose a file
alt.method
To remove a file from the package:
.
Then, r
Right-click on the file you wish to remove and use the pop-up that appears.
Log of changes
NMReDATA tags
(click on each header to unfold/fold its contents)
Other tags
Item contents
SDF header
Molecular structure display
Display:
Color code:
Display:
from:
explicitimplicit H
Spectra
spectrum
Coupling network
(you must first have displayed the couplings from the J or spectrum tag)
This is version 1.0 of this NNMReDATA J_reader.
For more information or contact, visit here.
What is currently parsed?
The NNMReDATA zipfile is read, all its contents are stored in memory and the directory is displayed in the lefmost column.
When clicked on an SDF item in the directory,
the structure is displayed in JSmol within the rightmost column;
all NRMeDATA tags and additional tags (both contained in the SDF file) are displayed in the central column. Test additional tags with Cyprinol
If the SDF includes several structural models, all will be loaded in JSmol (as frames); the tags will be separated in one section per model. Test with o-xylene (2 models, both with tags) and o-xylene-2 (2 models, only one with tags)
Right-click opens a menu with options (mainly intended for debugging):
Display the structure in JSmol within the rightmost column.
Save the SDF file to disk (includes structure and tags).
Display the text contents of the SDF file in a popup panel.
When clicked on a PNG item in the directory, it is displayed (image, thumbnail of a spectrum) in the central column (scaled 2x). Test e.g. with Mebeverin (inside pdata folders)
When clicked on a subfolder with numeric name in the file tree, it shows the thumb.png file that is inside.
When clicked on a DX, JDX or JCAMP item in the directory, its contents (JCAMP spectrum) are displayed in JSpecView within the rightmost column and also as plain text in the central column. Test with o-xylene
When clicked on a item in the directory, its contents are displayed in the central column (as plain text, unless it is known to be binary data).
When a structure is displayed in JSmol, the utility buttons on the right will work.
"show assignments" uses the contents in the NMReDATA_ASSIGNMENT tag. Assignments for implicit H's are added to the label of the atom they would be bonded to.
Ambiguous assignments (keyword "Interchangeable") are displayed with a reminder message, and may be coloured different via a drop-down menu. Same for "Equivalent".
"show couplings" uses either the contents in the NMReDATA_J tag or in the NMReDATA_1D_... spectra tags (with a drop-down selection when there are several 1D spectra) ; for implicit H's, coupling lines are drawn to the respective heavy atom using a different colour.
"add H's & make 3D" generates a 3D structure using either of 3 methods.
Warning when requested zipfile is not found.
Support for format version <1.1 (except for editing the tags) Test e.g. with benzopyrene.zenodo
A file (e.g. a JCAMP spectrum) may be added to the packaged NMReDATA zipfile. Files may also be removed from the package.
The contents of the NMReDATA tags, and other tags in the sdf file, may be edited and will be included when a new file is saved.
When the NMReDATA_ASSIGNMENT or NMReDATA_J tags are edited, the may immediately be reapplied to display on the structure.
New tags may be added to the NMReDATA set or the other tags set. Tags may also be removed.
A 3D structure model, constructed in the bottom "workshop" area, may be included as a second model in the sdf file. Copies of the original NMReDATA_ASSIGNMENT and NMReDATA_J tags from the 2D model will be modified to suit the newly added hydrogen atoms and will be included as data attached to the second (3D) model in the sdf file. An NMReDATA_VERSION tag is also generated for the second model.
Input files labelled * have been edited from the original ones (removing a root-level folder).
Using this tool?
Please cite our published description, https://doi.org/10.1002/mrc.5146 NMReDATA: Tools and applications.Magnetic Resonance in Chemistry 59:792-803 (2021)
Stefan Kuhn, Lianne H. E. Wieske, Paul Trevorrow, Daniel Schober, Nils E. Schlörer, Jean-Marc Nuzillard, Pavel Kessler, Jochen Junker, Angel Herráez, Christophe Farès, Mate Erdélyi & Damien Jeannerat
“The Workshop”:
Editing the model: guided conversion to 3D structure
This area is enabled from the "add H's and make 3D" button above.
Warning: Generation of 3D models does not guarantee the proper stereochemistry. It must be checked and validated by the user, aided by the tools below.
Add H's & make 3D:
Calculation will stop after 400 steps, or when −ΔE<0.001
Force stop
When result is not good enough, try further iterations of
Calculation will stop after 100 steps, or −ΔE<0.001
If stereochemistry correction is needed,
and then click on optimise
Refresh structure from main panel
Transfer structure to main panel (appended to the 2D model)
Return to main panel (do not apply changes)
Save to a 3D SDF file (not a complete NMReDATA package)
Manual designation of atom pairs as interchangeable (ambiguous assignment):
This will be saved in the NRMEDATA_ASSIGNMENT tag of the 3D model.
You should
1);
2) click on 2 atoms;
3) the result.
Manual designation of atom pairs as equivalent (known to have same chemical shift):
This will be saved in the NRMEDATA_ASSIGNMENT tag of the 3D model.
You should
1);
2) click on 2 or more atoms;
3) the result.
Load your own NMReDATA zipfile:
If local, it must be in the same folder.
choose a file
This is version 1.0 of this NNMReDATA J_reader.
For more information or contact, visit here.
