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

Chainbow
Useful to highlight order of structure elements in primary sequence (red N-terminus to blue C-terminus)

Secondary structure
Useful to indicate general structure (α-helices in red, β-strands in blue)

Specific features
Useful to indicate key features of interest (substrate in black, with active site triad residues in red)

Surface
Useful for proteins whose surface is key to its function (can sometimes be aided by cut-aways)

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 {{PDB}} identifier at end of caption

Example pymol code

#Ray tracing settings
set antialias,      2
set ray_trace_mode, 1
set specular,       0.25
util.ray_shadows('light')

#Cartoon looks
set ribbon_radius,             0.05
set line_radius,               0.1
set stick_radius,              0.2
set dash_color,                black
set dash_radius,               0.02
set dash_width,                1
set dash_gap,                  0.25
set cartoon_side_chain_helper, 1

#Correcting default Colours
set_color deepblue  = [0.05 , 0.19 , 0.57]
set_color marine    = [0.02 , 0.50 , 0.72]
set_color lightblue = [0.50 , 0.70 , 0.90]
set_color forest    = [0.10 , 0.50 , 0.10]

# Colour by secondary structure
colour red,   ss h
colour blue,  ss s
colour white, ss l+''

# Colour disulphides
show sticks,        (cys/ca+cb+sg) and byres (cys/sg and bound_to cys/sg)
set stick_radius,   0.15
select disulphides, resn cys&sc.
colour yellow,      disulphides

ray

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:

Secondary structure	Color	Example
Loop	#FFFFFF
α-helix	#FF0000
β-sheet	#0000FF
Disulphide	#FFFF00

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:

Protein feature	Color	Example
Main protein	#FFFFFF
Catalytic site/residue	#FF0000
Binding site/residue	#0000FF
Ligand/substrate	#000000
Cofactor	#FFFF00
Inhibitor/activator	#009900

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).

Cells

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.

Eukaryotic cell (showing cellular locations)

Cellular location	Color	Example
Outside Cell	#B9DEE1
Cytoplasm	#EBEBCC
Nucleus	#D0C4D1
Mitochondrion	#F7955B
Mitochondrial Matrix	#FCBC86
Chloroplast	#75C594
Endoplasmic Reticulum	#67A6CC
Golgi	#7A6BAB

Membranes

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

Level of detail	Description	Uses
High detail	Shows lipid layers, molecules (head and tail)	Transmembrane proteins, Fluid mosaic model
Medium Detail	Differentiates between lipid bilayers and single layers	General cellular process. Molecular interactions.
Low detail	Does not discriminate between multiple membranes.	Process such as Mitosis, Meiosis. Basic cell structure

Special Symbols

Name	Example	Description
ATP (NTP)		used in reactions equations
ADP (NDP)		used in reactions equations
AMP (NMP)		used in reaction equations
CO₂
FADH₂
FAD
Inorganic Phosphate
H⁺
H₂O
NADH
NAD+
NADPH
NADP
O₂
Phosphate
Pyrophosphate
Ribosome

Image upload

Upload your images to our Gallery at:

and also, please categorize them here: