Difference between revisions of "Jmol"

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(Replaced content with " === Technical test pages === Jmol testpage. Demo page by Angel Herraez.")
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<span style="color:#FF8C00">  '' 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)'' </span>
[[compatible software|''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.
=== 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 (<jmolSmiles text="example">aspirin</jmolSmiles>), 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...
=== Installation ===
For local installation:
1) download the last (?) version of the JSmol package - testing was done with version ???
2) save [http://www3.uah.es/nmr_e_data/reader/reader.htm the main page]
=== Funding ===
This development was funded, in part, by the University of Geneva, Gr. D. Jeannerat, in spring 2019.
=== Technical test pages ===
=== Technical test pages ===

Revision as of 10:52, 23 October 2019

Technical test pages

Jmol testpage.

Demo page by Angel Herraez.