> What we would like to do now is figure out a simple way to help users > quickly correlate peaks with atoms or vibfations. This is probably a > WebExport sort of functionality, I don't exactly know. All ideas are > welcome. The output would be a JCAMP-DX file. Looking for volunteers > for that. Should be a publication, I would think.... >
Very nice idea, to make Jmol talk to Jspecview! In 2003 we tried to make this work for (then) MDL Chime and Jspecview with some success and transferred the files to work with Jmol now. First we had to convert the (so-called) jcampdx files (or the original file formats called "ASCI-Export") of the instruments involved in taking the spectra to jcampdx format (the hard part). This and annotating the spectra had to be done manually. So it was a tediuos work to do (not covered by the grant for our project) and we limited our efforts to very few examples. We did not use MOL files but PDB instead (because we tweaked the pdb specification to annotate 3D-models with a colour representation of molecular interaction potentials, which we could not do with MOL files), but you can see these files in Jmol / Jspecview (somewhat outdated versions I think) at http://www.oc-praktikum.de by selecting NOP-Nr.: 2003 or 1001, then Analytics -> 1H-NMR or 13C-NMR -> use the link on the right side called "interactive spectrum" Structures are geometrically optimized with MOPAC. Spectra are measured (not simulated) and not everything is correlated to the structure. If you are interested you can get the annotated jdx files and the pdb. There may be an easier and better way to do this all, if your plan works out. > In addition, if anyone already has correlated data -- NMR spectra in > JDX format with known mapping to atoms of a specific MOL file -- we'd > like to know about that. Does anybody have anything like that? We're > also looking for net-based applications that could, for example, be > sent a MOL file and have a simulated HNMR or CNMR spectrum returned, > packaged in JDX format, with the incorporated ##$Models and ##$Peaks > records. Any suggestions? > > Bob Hanson > > Reinhold Störmann ------------------------------------------------------------------------------------------ Dr. Reinhold Störmann University of Bremen - Center for Environmental Research and Sustainable Technology Leobener Str. D-28359 Bremen Germany ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
