This is a scrapbook with propositions about the integration Jmol with NMReDATA. 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)
We are working on the interactions between NMReDATA and Jmol (and vice-versa).
Jmol as visualization tool for NMReDATA
- 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.
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...