next up previous
Next: MDD Calculation Up: README Previous: Process the Directly Detected

Convert NMRPipe File into MDD Format

In this step you need to produce a file directly used as input for the actual calculation program. You need to specify the input file (i.e. output from Step 4) and the output file (i.e. input for Step 6). There are two versions of the calculation software: one uses MPI for parallelization of the task on multiple processors, while the other can only use one processor. MPI version has the advantage of treating the whole spectrum in one go, but it is usually much slower. It is recommended that you use the single processor version. Since majority of NMR spectra are too large for only one processor, it is necessary to subdivide the spectrum into smaller overlapping regions and treat each region separately. Each region contains complete indirect dimensions and a portion of the acquisition dimension. E.g., if you process $^{15}$N-NOESY-HSQC (say, between 11 and 5.5 ppm in direct $^{1}$H) and would like to subdivide the spectrum into 16 regions, each region would be just under 0.5 ppm wide. Some overlap is usually desirable, so that edges of each region could be discarded later, when the result is put back into one spectrum. It is recommended to use region size of around 0.3-0.4ppm and the overlap to be on the order of 0.1ppm. These values will be adjusted to make the regions with integer number of points.

You can optionally provide a schedule file, which is produced together with the VDLIST. There is no schedule file for Varian data. Press the CONVERT TO MDD button and check the console window for progress output and any error messages. Then move forward.


next up previous
Next: MDD Calculation Up: README Previous: Process the Directly Detected
Aleksandras Gutmanas 2009-01-26