Revision as of 19:12, 28 October 2019 by Angel.herraez (talk | contribs) (Installation)
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Ongoing discussion on the jmol-users @ lists.sourceforge.net and private communication between Damien Jeannerat and Angel Herraez (if you want to join, you are welcome)

J-reader is webtool that can be accessed through the web or installed on a local computer. In both cases, the programs is running on the users's computer. Not data (structure, etc.) are send to any server via the net.

This page is under construction and will be improved...

Main features

  • display the structure(s)
  • display the data in the signal assignment tags (NMREDATA_ASSIGMENT )
  • display the data in the J-coupoing assignment tags (NMREDATA_J)
  • for each NMREDATA_1D tag, display the 1D spectrum (pop-up window) and add as overlay the data found in the tag (chemical shifts, couplings, multiplicity, on top of the spectrum, labels, integral, etc.)
  • for each and NMREDATA_2D tag, display the 2D spectrum (pop-up window) and add on top the spectral data found in the tag (list of correlations vertical and horizontal lines for each "label" and dits when the correlation was listed in the tag)

2D to 3D conversion

JSmol can display 3D structures (example), but as now the NMReDATA .SDF files include "flat" structures.

A first step, we could say that when there is no 3D structure in the sdf file, we use Jmol the build-in addition of H and “optimized” 3D structure, allow to save it, just to get started. I think that renumbering the atoms for proper reference will not be impossible…(via a reference table if direct correction of the NMREDATA_ASSIGNMENT table is not possible. We will see later if other tools should be used to generate a 3D or if we can develop more the ones in J-mol to make the process better (user) controlled.

Difficulties - when H atoms are implicit, renumbering is necessary - it could be done...


For local installation:

Download the J_reader package that contains a copy of the web application and ancillary files. Extract everything.

This download uses JSmol, a part of the full Jmol distribution, version 14.29.46.
It does not include any of the sample files used for demonstration by the web application.

The files should be arranged according to this schema:

  • reader.htm (the interface)
  • combined.js (utilities; contains code from jsTree, jQueryModal, AlertifyJS)
  • combined.css (ditto)
  • img/ icons used in the page
  • JSmol.min.js (main file of the JSmol library)
  • php/jsmol.php (a component from JSmol library)
  • js/JSmolJSV.js (a component from JSmol library; other files in that folder are not needed)
  • j2s/ (components forming the JSmol library; includes about 1300 files and subfolders)

The application works well from a web server; from local disk, it will work at least in some browsers. When running locally, due to security policy of the browsers, loading of data files is restricted to the folder where the htm file is (sometimes it works as well for subfolders and parent folders). Additionally, some browsers will require setting internal parameters (in about:config or equivalent feature), like security.fileuri.strict_origin_policy = false or privacy.file_unique_origin = false


This development was funded, in part, by the University of Geneva, Gr. D. Jeannerat, in spring 2019.

Main features

This work was presented at the 1st NMReDATA symposium in sept 2019.


We thank Marion Pupier for multiple examples of NMR records used for this work.

Technical test pages

Jmol testpage.

Demo page by Angel Herraez.