Multidimensional decomposition (MDD) is a mathematical tool for processing 3D or higher dimensionality NMR spectra. For theoretical background, examples and applications, please see the references. For the purposes of this text, it is important to understand that MDD is able to reconstruct a complete spectrum from approximately 30% of FIDs that are actually recorded, the so called sparsed or non-uniformly sampled spectrum. The program MDDGUI combines a few scripts to prepare the input and process the output of the actual MDD calculation. So far it works only for 3D Bruker spectra. The whole process currently has 8 steps as follows
When recording the sparsed spectrum, one needs to indicate which FIDs are to be recorded. In our lab MK rewrote the standard pulse sequences using an additional file, VDLIST, which does exacly that. If the entry in VDLIST is '1u', an FID pair (Re and Im or Echo and Antiecho) is skipped, if the entry is 3u, it is recorded and stored in the SER file. To be able to process the spectrum you must have the correct VDLIST file.
The first step of the processing is thus reaaranging the recorded FIDs and putting them into a new file, similar in structure to SER. Fill out the required fields on the first work page of the MDD program. Most often, you would need to use the prefilled values. You need two input files: SER and VDLIST and one output file SER.SP. Press the INSERT ZEROS button and check the console window for any error messages. Then move to the next page. For the purpose of clarity, this text will assume that the FIDs are now rearranged into SER.SP file.
The second step is to convert the Bruker-style data into NMRPipe format. On the second page of the MDD wizard edit a FID.COM script for BRUK2PIPE conversion just as you would do for a regular spectrum. Most parameters should be read correctly already, but double check the acquisition mode for the indirect dimensions as these are often difficult to get right in a sparsed experiment. Make sure that
Save the conversion script and perform the conversion by pressing the corresponding buttons. Then move to the next step.
The third step is required to determine the processing parameters for the directly detected dimension. To allow to do so, the first plane is always recorded completely, i.e. all FIDs are present. Edit the prefilled NMRPipe script to suit your case. E.g., change input file, region of interest, phase corrections, etc. You might need to create a new directory for the output file. This step is interactive, in the sense, that you can modify the necessary parameters a few times and check the result with nmrDraw, just as you would normally do with a regular spectrum. Script lines between the capitalised comment lines are copied for the next step's script, which is why DO NOT DELETE OR MODIFY these comment lines. When you are satisfied with the phasing, move to the next step.
In the fourth step only the directly detected dimension is Fourier transformed for the whole spectrum. The indirect dimensions are incomplete and should not yet be transformed. The script is copied from the previous step, but you should still double check the relevant parameters, phase corrections being the most important. In this step you also make the decision on the size of the region you wish to process, thus change the corresponding line accordingly. Save the script and process the spectrum. The output should be in the form of a single file rather than set of planes, so don't change that. When done, move to the next step.
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 parallelisation 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. 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 directly detected dimension. E.g., if you process 15N-HSQC (say, between 11 and 5.5 ppm in direct 1H) and would like to subdivide th espectrum 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.
You can optionally provide a schedule file, which is produced together with the VDLIST. Press the CONVERT TO MDD button and check the console window for progress output and any error messages. Then move forward.
The actual MDD calculation is taken out of the GUI wizard because it can take a long time to perform and it may be annoying to keep the graphical program idling. In addition, you may wish to perform the calculation on a more powerful machine or a cluster. You should thus transfer the output file from Step 5 to the desired location and start the calculation. The detailed instructions are repeated in the information window of the user interface and are given here for reference. You can fill out the relevant fields below the information window, and press the CREATE COMMAND FOR CALCULATION button. This will create a file with the correct command, which you can run or copy into command line.
In this step you have to transfer the results from the res.dat file (or its copy) back to NMRPipe format, filling in the missing FIDs by calculated values. The input files are the output from Step 4 (same as input for Step 5) and res.dat file for MPI version or the region list file for the multiregion version. The output is a new reconstructed NMRPipe file with the directly detected dimension Fourier transformed. Press the RECONSTRUCT button and check for progress output and any error messages in the console window. Move to the last step.
This is the final step of the processing. A sample script is given, which you sould modify to suit the circumstances and then use to finalize the processing, just as you would with an ordinary spectrum.
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