Smartnotebook: Folded Peaks

Note: I have had to test this functionality with simulated data. If you have some real data that you can donate to this project then that would really help to make sure folded peaks works correctly. Thanks.

If your peakpick files contain folded peaks, then you need to tell smartnotebook about them.

One of the problems peakcon has is to recognize connectivities that involve folded peaks. It is the task of smartnotebook to take the original peakpick files, apply the appropriate modifications, and then let peakcon do its thing on these new peaklists. Smartnotebook does not know what the folded peaks are, so it tries to present an environment that allows the user to easily find and specify the folded peaks. Here is how it works.

1. Click on the "Options" menu and select the "Folded Peaks..." entry. You will receive a popup window that indicates your current folded peaks. Let's assume that you want to add a folded peak so click the "Add" button.

2. At this point, the software needs to know 3 things about your designated folded peak:
   1. peakId
   2. peaklist
   3. atom name

   In the example that follows, the user is designating peakId 2 of the reference spectra as being folded in the Nitrogen dimension (just pretend that it is). The peakId was either typed by the user or set by one of the functions in the smartnotebook "Reference Id" menu.

   

   By designating the folded peak above, the software needs to search the other peaklists for corresponding peaks that will also need to be folded.

   The "Closest Choices" field means the closest 'n' choices to your selected peak in each peaklist will be displayed, usually 4 is a high enough number. If you select "opposite" phase, the intensity of the folded peak will be multiplied by -1.

   At this point, one can click the "Search" button. You should see a new popup window similar to the one below.

   

   It is now your job to select each peak which you believe is folded and click "Add" which adds it to your current folded peak list. Depending upon the spectra type, multiple peaks may be folded in the same spectra. Click the "Done" button when there are no more peaks to add.

   

   If you go back to the original folded popup window as shown in the figure above, you can see how smartnotebook shows you the exact nature of the adjustment to your peakpick files. In the above example, columns 3-6 show you the original peak, columns 7-10 show you the adjusted folded peak. If at any time you realize a mistake has been made, select the offending peak line and hit the "Delete" button.

3. Now repeat this process for the remaining folded peaks. It is the user's responsibility to verify the folded peaks, smartnotebook does not have any knowledge about folded peaks.

4. When you exit this window by clicking the "Quit" button, you are asked if you want to save the changes. When you confirm the changes, all the folded peakpick files are updated and all the connecivity files are re-calculated.

Smartnotebook keeps track of the folded peaks in the spectrally named "*.fold" files in snb.out. Your original peakpick files are never modified. Click here to see the example hncacb.fold file with folding in the nitrogen dimension.

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