Figures with CCPNmr Analysis

There is quite a lot of customising you can do in Analysis to create really nice publication-quality images of your spectra which only need a little bit of tweaking in a graphics programme such as Adobe Illustrator or Inkscape (free from inkscape.org).

Contours

The way you have your contours set up to view your spectra may not be the best set-up for a publication or presentation slide image. Go to the Contours toolbar and select More.. . Alter in particular the Number of levels (actually the maximum number of levels) and the Level multiplier (how closely the levels are drawn). Lots of close levels will give a blob appearance, few close levels result in a ring appearance and few spaced out levels will make each contour individually visible.

Peak Labels

By going to Peak -> Draw Parameters you can select which piece of information is placed in the peak label. I find Minimal Annotations is often very useful for images – it gives you just the 1-residue amino acid code and residue number. If you don’t want any peak labels then you can switch them off as part of the printing options below or simply de-select all peak lists in the Peaks toolbar of your spectrum window. The Draw Size tab lets you alter the size of the little cross used for each peak. If you would rather have a + than a x, then go to Peak -> Peak Lists and change the Peak Symbol. You can also change the peak symbol and annotation here if you wish.

Peak label placement can either be sorted out later in an external programme (see below) or you can do (at least some of it) in Analysis using the following keyboard shortcuts: w automatically places the peak labels of all selected peaks such that they don’t overlap (note that the way this is done depends on your current zoom level. W resets the peak labels to their original position. q moves the peak label of the currently select peak to the current mouse position. I usually start by using the w option, fine tuning this with q and then finalising it all in an external programme (see Further Customisation below).

Printing Options

Go to Window -> Print Window and use the drop-down menu at the top to choose the Window you would like to print from and then further customise your image using the four tabs available.

Options

Enter a file name and (optionally) a title and axis labels. Unfortunately, super/sub-script and Symbol font are not available, so if you want to use these in your title or axis lables you will need to add these later in another programme (see Further Customisation below).
Select your paper size, orientation, style and format as desired. I usually go for the defaults of A4, Landscape, Colour and PDF.
Ticks: Select Location as Outside and placement as Bottom and Right only. Change the Tick Font and Spacing if desired – manual tick spacing can be quite useful. I personally don’t like the default tick length and normally set this manually to 8 and 4 for the major and minor ticks, respectively.
Scaling: The default 70% scaling will generally fit your spectrum nicely onto a piece of A4. But you can easily change the scaling yourself be selecting Cms/unit. For each axis you can now select how many cms per ppm you want.
Include or exclude the Time and Date and File Name as desired.
I recommend setting the line-width to 0.5, otherwise your lines will be very thin and difficult to see (especially if you want to use the image in a presentation).

Spectra

By default, Analysis will include all spectra which are currently visible in the window you are printing. But you can override this (just make sure you select Use below settings when printing) and select/deselect positive and negative contours for each spectrum in that window.

Peak Lists

By default, Analysis will print all peak lists which are currently visible in the window you are printing. Override this and alter the font type and size if you like (again make sure you select Use below settings when printing).

Region

By default, Analysis will print the region currently visible in the window you are printing. You can override this if you like. Normally this can be done very easily with the Min and Max option. But if you are printing an individual strip, then Centre and Width is rather useful here.

Finally click on Save Print file. Inspect your image and make changes if desired.

Further Customisation

You can further customise your image using programmes such as Adobe Illustrator or Inkscape (free from inkscape.org). Using either of these programmes you can simply open a pdf file generated by CCPNmr Analysis. Rotate it if necessary. Select the image and then Ungroup (multiple times) in order to manipulate individual elements of the figure. I usually use this step in order to finalise peak label positions (including the little arrows) and do the axis labels using superscript and Symbol fonts. Sometimes it is also necessary to remove the coloured frame which Analysis places around the visible part of each spectrum (it depends on your zoom level as to whether this has been printed or not).

NEW!

Solid-state NMR spectroscopists may be interested in my recentarticle on ‘Solid-state MAS NMR resonance assignment methods for proteins’published in Progress in NMR Spectroscopy (free download until 27 July 2018here).