Figure Preparation in the Foster Lab

Preparing scientific figures for manuscripts, presentations and grant applications

Glossary

  • Vector format: a graphics format in which images are produced via commands (draw line from x1,y1 to x2,y2). This format can be scaled infinitely with no loss of resolution.
  • Raster or bitmat format: Images composed of a grid of pixels in which each pixel has a different color. The resolution of the image is set by the number of pixels (e.g., 150 dpi)

Preferred Software

  • Graphics anotating: Powerpoint, Illustrator
    • Alternatives: LibreOffice Presenter, Keynote, Inkscape
  • Image manipulation: Graphic Converter (Mac), GIMP (LINUX), Photoshop

General rules of thumb

  • Use Helvetica or Arial for figure text
  • Use sufficiently large text so that it can be clearly read when printed at the intended size
  • Do not allow figure elements to clash/overlap (annotations, lines, images, legends)
  • When possible, prepare figures using vector format, not raster/bitmap
  • Figures should be prepared separately, including annotations/labels, then embedded intact into a text document – do not try to edit a figure within a word processing program!
  • Use black and white unless color is necessary to illustrate a point

Preparing nD NMR spectra

  • Be sure to simplify the figure to focus the reader’s attention to the spectral features of interest – do not expect a reader to interpret the spectrum on their own. This usually means zooming-in on a region of interest, at the expense of the full spectrum
  • If a full spectrum is to be shown, minimize blank space, and ensure that peak labels do not overlap
  • From the NMR program, output the spectrum in scalable vector format (usually PS or PDF)
  • Import the file into software that can edit vector graphics files (Adobe Illustrator, Inkscape)
  • Add/manipulate text and annotations in vector format – change fonts as required
  • Crop/expand figures as needed so to minimize blank space around the figure
  • Reduce the number of contours and/or inter-contour spacing to minimize file size
  • Save annotated spectra in both vector and image formats. The image files should have a minimum resolution of 150-300 dpi for items to be printed.

Preparing images of structures (mostly via PyMOL)

  • Use PyMOL’s ray-trace mode
  • in ribbon diagrams, when showing sidechains via sticks, hide backbone atoms (proteins: n, o and c; NA: o1p, o2p, p), unless they are needed to illustrate a point
  • Minimize blank space
  • Add annotations in vector format (Powerpoint or Libreoffice Presenter preferred; Keynote, Illustrator or Inkscape OK)
  • Generate high-resolution bitmap image (png, jpg or tiff; 300+ dpi).

Importing into documents

  • Copy-pasting of images into documents often has unpredictable results.
  • DO import/insert figures into the document
  • Do NOT draw line borders around embedded images

Figure legends/captions

  • Figure legends should describe the figure and the point to be made