Examples

Protein L

Having processed a spectrum and picked peaks in NMRPipe :

peakipy read test.tab test1.ft2 pipe --y-radius-ppm 0.35 --x-radius-ppm 0.035 --show --struc-el disk --outfmt csv

Since the dimensions are in order ID,F1,F2 (Z,Y,X) there is no need to use the --dims argument.

A contour plot of the spectrum with clustered peaks (color coded) is generated along with a .csv file of the same name as your original peak list (i.e test.csv).

To fit the peaks simply run :

peakipy fit test.csv test1.ft2 fits.csv --lineshape G

the --lineshape G option is used to fit the peaks to a Gaussian lineshape (in both dimensions).

If you have a vclist (or equivalent) then you can add this to your output data so that the planes can be sorted based on the vclist column.

peakipy fit test.csv test1.ft2 fits.csv --lineshape G --vclist vclist

For interactive inspection of fits, run peakipy check:

peakipy check fits.csv test1.ft2 --outname plots.pdf --clusters 30 --clusters 32 --show --first

Adding the --individual and --label flags will add the simulated lineshape for each fitted peak as a 3D surface along with the assignment labels.

Omitting the --first flag will result in a multi-page pdf with each plane plotted on a seperate page. If you do not want to interactively display the fits then just omit the --show flag. If you would like to plot the fits for all peaks then omit the --clusters flag.

If you find that you need to adjust the parameters of specific fits you can run :

peakipy edit test.csv test1.ft2

Which will open a Bokeh server in which you can adjust individual parameters on each peak.

To save your edited peak list just click Save. You can open it again later :

peakipy edit edited_peaks.csv test1.ft2

Your fitted intensities can be accessed conveniently through the fits.csv output file using pandas or a spreadsheet.