Wikipedia:WikiProject Molecular Biology/Diagram guide

File Format
The preferable image format is SVG, since it is a scalable vector format, specifically designed for the internet. It is particularly useful for cellular processes since these tend to be diagramatic in nature. It also lends to easier editing. Raster image formats are also acceptable (e.g. for protein structures), however remember that image quality diminishes with scaling so upload a high-resolution image if possible (>1000px wide). When using a raster format, PNG is preferable to JPEG.

Protein structures
The main thing to consider when creating images of protein structures is "What are we trying to highlight in this image?". With this in mind, here are the MCB wikiproject's formatting recommendations.

In general proteins should ideally be:
 * Rendered using PyMol
 * Oriented automatically unless there is a particularly characteristic orientation to use PyMol wiki
 * Ribbon cartoon representation PyMol wiki
 * White background (the rest of the article is black text on a white background)
 * Ray trace mode 1 (a black outline makes perspective clearer) PyMol wiki
 * Antialias 2 (high quality line rendering) Pymol wiki
 * Rayed (generate high resolution image) PyMol wiki
 * State the identifier at end of caption

Colouring
The use of colour is the main way of conveying information about a protein structure, since otherwise most proteins just look like a ball of spaghetti. There are a few options for using colour to clarify the overall protein structure, and some options for highlighting particularly significant features.

Overall protein structure
Protein structures have traditionally been coloured using the 'chainbow' effect which creates an N-to-C terminal blue-to-red colour gradient. This can help to show how protein sequence relates to tertiary structure.

Another option is to instead colour by secondary structure, which can help to illustrate the general fold class and broad structural features of a protein (which is often more useful than focussing on primary sequence order). The following standard colour scheme is recommended:

Highlighting specific features
Often it is useful to specifically highlight key features of a protein such as its active site or a bound ligand (for example see enzyme article). In this case, colouring most of the structure white draws attention to the important residues, regions or segments. The following standard colour scheme is recommended:

Surface representations
Although the ribbon cartoon is the most common way of displaying a protein structure, a protein whose surface shape clearly affects its function may best be shown as a surface. For example, a surface representation may help demonstrate the contours of a binding pocket or size of a membrane protein pore. Sometimes a cutaway is useful to reveal hidden internal features (pymol wiki).

Color Scheme
In order to maintain a standard for Cell and molecular biology articles a standard color scheme should be used. The accepted colors for cellular locations are described in the table. Colors for other components, such as molecules, can be chosen at the discretion of the designer, however, the following should be considered:
 * Colors should be chosen so that they contrast with existing colors in the image
 * Colors should be chosen such that text can be easily read on it.
 * Text should be black
 * Arrows should be black, however, different colors may be used to describe a set of processes or to contrast colors.

Membranes
The level of detail for a membrane should be only what is necessary to describe the cellular process.