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.
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:
{{
PDB}}
identifier at end of captionExample pymol code
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#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 |
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.
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 |
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 |
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).
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:
Cellular location | Color | Example |
---|---|---|
Outside Cell | #B9DEE1 | |
Cytoplasm | #EBEBCC | |
Nucleus | #D0C4D1 | |
Mitochondrion | #F7955B | |
Mitochondrial Matrix | #FCBC86 | |
Chloroplast | #75C594 | |
Endoplasmic Reticulum | #67A6CC | |
Golgi | #7A6BAB | |
The level of detail for a membrane should be only what is necessary to describe the cellular process.
Level of detail | Description | Example | Uses |
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High detail | Shows lipid layers, molecules (head and tail) |
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Transmembrane proteins, Fluid mosaic model |
Medium Detail | Differentiates between lipid bilayers and single layers |
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General cellular process. Molecular interactions. |
Low detail | Does not discriminate between multiple membranes. |
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Process such as Mitosis, Meiosis. Basic cell structure |
Name | Example | Description | |
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ATP (NTP) |
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used in reactions equations | |
ADP (NDP) |
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used in reactions equations | |
AMP (NMP) |
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used in reaction equations | |
CO2 |
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FADH2 | |||
FAD | |||
Inorganic Phosphate |
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H+ |
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H2O |
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NADH | |||
NAD+ | |||
NADPH |
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NADP |
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O2 |
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Phosphate |
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Pyrophosphate |
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Ribosome |
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