Revision as of 18:59, 4 April 2019 by Admin (talk | contribs) (Jmol as visualization tool)
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This is a scrapbook with propositions about the integration Jmol with NMReDATA. Ongoing discussion on the jmol-users @ and private communication between Damien Jeannerat and Angel Herraez (if you want to join, you are welcome)

We are working on the interactions between NMReDATA and Jmol (and vice-versa).

Jmol as visualization tool

Jmol includes javaScript functions to visualize 3D structures and spectra (1D and 2D).

A project would be to develop a web-page to load a zip file containing:

  • a chemical structure (2D or 3D or both...)
  • NMR spectra (they will initially be in the Bruker format be we could convert them into Jcamp for compatibility with jSpecView
  • a NMReDATA.sdf file including tags providing the assignment of the details about each spectrum.
  • possibly other things, such as IR spectrum... or other documents ? text files ?

The main idea is to

  • display the structure(s)
  • display the spectra (pop-up window when requested)
  • display on control panel to select which information from the assignment data to display on the structure and the spectra, and allow interactions (rolling on a C on the structure should show the correponding signal in the relevant NMR spectra.

The main work for the development of a reader of NMReDATA would be for JSmol to show the 2D correlation found in 2D spectra (COSY, HSQC, HMBC, NOESY) on the visualized 3D model. These information is in the "NMREDATA_2D_…” tags (for example the NMREDATA_2D_13C_NJ_1H tag shows the list of pairs of H/C for which signals were found in the HMBC experiment). The reference to the atom index of the molecule is in the NMREDATA_ASSIGNMENT tag). The display of the correlations could be turned on/off from a main panel… A step that could come only after we make decisions with respect to the spectra (conversions to Jcamp) - probably in 2 weeks. At that point the idea will be to also display the NMR spectra (JspecView) that will be found in the same folder as the NMReDATA.sdf file and be referred to using links from the NMReDATA.sdf file.

We should add, on the spectra displayed by Jspecview, the assignment information found in the tags about each spectrum (the assignment of the multiplets from 1D spectra (for example in the NMREDATA_1D_1H tag: list the J coupling measured, the integral, the label used by the user, etc.), and for 2D, the pairs of correlations mentioned above in this e-mail, the labels of the relevant signals.

I see all this to be working on a browser, with different windows/part of window for the

  • the 3D structure (maybe one with the 2D if this is easy)
  • multiplet 1D and multiple 2D spectra
  • a control window to switch what we see/don’t see and read/save the files

There again, a first step could be to “just” visualize the content of the NMReDATA.sdf file, a second would be to edit (by allowing interactions to add/remove/edit content.

2D to 3D conversion

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

We therefore proposed to allow the inclusion of 3D structures in NMReDATA .sdf files.

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...

simple demo Jmol visualization

Jmol testpage.

Demo page by Angel Herraez.

Jmol testpage accents.