Wikipedia:WikiProject Molecular and Cellular Biology/Diagram guide

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File Format[edit]

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, if we decide to change aspects of the scheme. Raster image formats are also acceptable, however one must remember that image quality tends to diminish with scaling. When using a raster format, PNG is preferable to JPEG. See Wikipedia:Preparing images for upload

Image upload[edit]

Upload your images to our Gallery at: and also, please categorize them here:

Protein structures[edit]

Overall protein structure
Overall protein structure
TEV protease based on 1lvb (N-C terminus, blue to red)
Feature highlighting format
Highlighting specific features
TEV protease (white) complexed with peptide substrate (black) with active site triad residues (red) based on 1lvb

In order to present a unified format for protein structures, the two formats below are recommended. For the discussions that lead to these guidelines, see the Wikiproject discussion, Wikiproject discussion archive (2008), and this page's discussion

  • Rendered using PyMol
  • Oriented automatically (Pymol-optimised screen real-estate) PyMol wiki
    • Unless there is a particularly characteristic manual orientation to use
  • Cartoon representation PyMol wiki
  • White background
  • Ray trace mode 1 (black outline) PyMol wiki
  • Antialias 2 (high quality line rendering) Pymol wiki
  • Rayed (generate high resolution image) PyMol wiki
  • State PDB number in caption

Overall protein structure[edit]

In general, protein structures should be coloured using the 'chainbow' effect which creates an N-C terminal blue-to-red color gradient which can help to show how protein sequence relates to tertiary structure.

Highlighting specific features[edit]

When drawing attention to specific features of a protein or enzyme, the following presentation is suggested:


Protein feature Color Example
Main protein #FFFFFF
Active site #FF0000
Ligand #000000
Water #0000FF
Cofactor #009900
Inhibitor #FFFF00

Cells[edit]

Color Scheme[edit]

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 hybrid (showing cellular locations) by project member WikipedianProlific


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

Membranes[edit]

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

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


Special Symbols[edit]

Name Example Description
ATP (NTP) ATP symbol.svg used in reactions equations
ADP (NDP) ADP.svg used in reactions equations
AMP (NMP) AMP.svg used in reaction equations
CO2 Carbon dioxide symbol.svg
FADH2
FAD
Inorganic Phosphate Inorganic Phosphate symbol.svg
H+ Proton symbol.svg
H2O Water Symbol.svg
NADH
NAD+
NADPH NADPH symbol.svg
NADP NADP symbol.svg
O2 Oxygen symbol.svg
Phosphate Phosphate.svg
Pyrophosphate Pyrophosphate symbol.svg
Ribosome Ribosme symbol.svg