Peaks from NmrResidues macro
Much of the information in peptide spectra is redundant which means that you will not need all peaks or spectra to assign the atoms in a residue. However, once the atoms in a residue have been assigned, it is helpful to label all the maxima in your Spectra belonging to the atoms in this residue while you go on to assign other residues. You can do this by creating Peaks and labelling them with NmrAtoms (which are grouped into NmrResidues). A CCPN macro called peaksFromNmrResidues can help you do this quickly and efficiently without having to trawl through all the Spectra placing and labelling Peaks manually. (See below for some helpful nomenclature if you are still new to the program.)
Before you start, you should ensure that your Specta have been assigned their Experiment Types. Do this by going to Spectra / Experiment Types or using the shortcut ET.
To use the macro, go to the Macro menu and select Run CCPN Macros / peaksFromNmrResidues. In the resulting pop-up you can use drop-down menus to select the NmrResidue for which you want to pick and assign peaks. You can also select the ChemicalShiftList from which the peak positions (literally the Chemical Shifts of the NmrAtoms) should be taken. In many situations you may only have one ChemicalShiftList, anyway. You can then select the Spectra where you want to pick and assign peaks (note that not all Experiment Types, e.g. a 1H-13C-HMBC, may be supported at present). Next, select whether you want to place the newly picked peaks into the first, last or a new PeakList of the selected Spectra. You can now select the Peak Creation Method, i.e. whether to place your peaks at the exact position specified by the Chemical Shift List (this will not change the Chemical Shifts of your NmrAtoms, but the peaks will not necessarily lie on top of the exact maxima in your spectra), or whether you want to Pick the Peaks with a small area peak pick (which will fit the peak positions to the maxima in your Spectra, but may change the Chemical Shifts in your Chemical Shift List, since these are averages). Further options include limiting the creation of peaks to those with aliphatic NmrAtoms and checking for existing Peaks so that you don’t double up on any existing peaks. The option to assign Peaks to new NmrResidues should only be relevant when using Reference Chemical Shifts as described below. Finally click on Create Peaks to execute the macro.
Using the macro to place Reference Chemical Shift Peaks
We have created a NEF file containing a 20-amino acid chain with all the Reference Chemical Shifts. You can import this into your project and use it to mark the reference chemical shifts in your Spectra (see our Reference Chemical Shifts webpage for more information on this), but also to create peaks at these positions which you can then easily shift into place to match the maxima in your Spectra.
Import the .nef file by going to File / Import / Nef file, using shortcut IN or by dragging the .nef file into your project. If asked, select to Import the file and then in the NEF Import dialog box tick RefChemShifts.nef on the left hand side which will automatically tick the Chain and ChemicalShiftList below. Click the Import button and you will see that a new Chain, ChemicalShiftList and NmrChain have been added to your project.
Tp place Peaks Run the peaksFromNmrResidues macro as described above, but make sure you select one of the NR:RefCS NmrResidues and the CL:RefCS ChemicalShiftList. Finally, you can select the assign Peaks to new NmrResidues option to make sure that your Peaks will be created with the NmrChain and Sequence Code of the peptide you are working on.
Nomenclature
Peaks: these are the Peak objects (the little cross symbols) that are placed on the maxima in Spectra. They are tabulated in PeakLists. Each Peak has a position associated with it. A Peak may also be assigned which means that it has a peak label (one for each dimension). The peak labels are the NmrAtoms which are grouped into NmrResidues. They correspond to actual (Molecular) Atoms in a peptide, protein or other molecule. Don’t confuse a Peak within the program with a maximum in a Spectrum which we naturally think of and colloquially refer to as a peak.
NmrAtom: these are essentially the peak labels used within the program. However, they are structured as having a Name, belonging to an NmrResidue with a Sequence Code and Residue Type which in turn belongs to an NmrChain. In that sense they obviously correspond to Atoms, Residues and Chains for your actual peptide or protein, but the Residue Type and Name are essentially free text boxes, so you can also be flexible about how you name them and don’t have to associate them with a particular real Atom if that information isn’t known during the assignment process, for example.
