peter murray-rust wrote: > I've had a long talk with Henry. Essentially his position is that he has > a method for calculation which gives significantly increased accuracy in > an automatic fashion. What I would suggest that Nick does is to use > Henry's method on a carefully selected subset of NMRShiftDB.
In fact, I should have stated more clearly that I'm very much in favor of having Nick do NMRShiftDB G03 calcs using Henry's method. The stuff that we've done is just supplemental. > Stefan says it isn't available. In any case is it Open? I think Henry > would contend his method would be an advance. The data are open and partly loaded into NMRShiftDB. I've written to Warren again (did this a couple of times already) to get the rest. But again, this is supplemental - let's go for your plan. >> I myself have been calculating about 2000 Gaussian spectra for >> NMRShiftDB on a 16-node cluster which came for exactly this purpose with >> my NMRShiftDB grant. > > Is this published? We don't want to pre-empt you. No, it is not published and I don't think it will. There was no rigorous selection of a reasonable starting geometry in my protocol, so I would have difficulties to justify my data. > I think this is a good idea and henry has been advocating it but Nick > doesn't have time to generate conformers. So we would stick with rigid > molecules. Ack > So I'll revise the strategy. The fundamentals are that it must be > automatic. Ack >> > * generate 3D coordinates > > Any suggestions here? No - our 3D generator is broken at the moment. >> > The immediate difficulties we can see are: >> > * not knowing the stereochemistry. *** WHAT IS THE POSITION IN >> > NMRSHIFTDB? We can filter out anything that has more than one >> > potential stereocentre. A lot of structures with stereocenters in NMRShiftDB have undefined stereochemistry. It would be good to generate all of them in 3D and do the calculation (in case of E/Z and diastereomers). >> > * assumptions about completeness of data in NMRShiftDB Not sure what that means. >> > * generating initial 3d coordinates. There are several simple >> approaches: >> > - use CDK - I think Christoph had something here? >> > - use the 2D coordinates for "flat" molecules >> > *** NEW APPROACHES - MUST BE BLUEOBELISK How about this newly discovered "RDKit" (or so)? See Noel's blog. Seems to have a BSD license 3D generator. Regarding the workup of the data: I would like to train our shift prediction machine learning methods with the GIAO data and see how that compares to the experimental data. Cheers, Chris -- PD Dr. Christoph Steinbeck Lecturer in Chemoinformatics Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax: (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Blueobelisk-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
