Hello!
I am new to CCPN and so I’m sorry if this has been covered in a different topic, I just haven’t found it.
I need to create an NCO peak list but the NCO spectrum has a lot of overlapping peaks, so I wanted to use the NCOCX spectrum to find at what N value the sidechain peaks are at their max and then trace that back to the CO diagonal and mark that position as a peak. I’ve looked through the NCOCX spectrum and see that not all sidechain peaks are at the exact same N value, or CO value, but they’re very close.
I was just wondering if I needed to write a macro for this, and if so, how I should start.
Also this is for solid-state NMR and I am using CCPN v3.1.
Thank you very much!
Maia
Hi Maia,
it all depends a little bit on exactly what is going on here.
If the issue is that your NCOCX and NCO spectrum don’t completely overlap, i.e. the referencing is slightly off between the spectra, then simply have a look at our instructions on how to reference spectra relative to one another at Spectrum Calibration. There are several different ways of doing this.
If your problem is that let’s say the N-CA-CB and N-CA-CG peaks don’t have the exact same N value, then this is normal and simply part of your experimental error. The program will always average your chemical shifts across all peaks. So you can simply take that average from the Chemical Shift List and place your NCO peak at this value if you like. I would probably just place these peaks manually, but you can use the command line in the python console if you wish:
get('PL:nco.1').newPeak([177.92, 120.78])
where PL:nco.1 is the peakList into which you want to peak to go.
See our background information on Chemical Shifts for more information about how the program handles Chemical Shifts.
Another option you available to you, if you already know your N and CO chemical shifts from other spectra is to create a synthetic PeakList automatically. So if you right-click on your Chemical Shift List in the sidebar you can select Create Synthetic PeakList. And then you can select NCO from the drop-down. This will create a new dummy spectrum with a peakList in it which you can easily copy to your spectrum of interest.
I hope these suggestions help. If you can be a bit more specific about exactly what your aim is, then I may be able to make other suggestions, too.
Vicky
Hi Vicky,
Thank you for your quick response! I’d say that the problem is more the second one where the peaks from one residue don’t all appear at the same N, which isn’t that bad.
The option of creating a synthetic PeakList sounds ideal. I mostly don’t want to do this manually because there are over 250 residues and none of them are assigned.
And sorry I wasn’t very clear with my goal, I want to create an NCO peak list (I don’t need assignments) from an NCOCX spectrum.
Thank you!
Maia