Wikipedia:Wikiproject Metabolic Pathways/style guidelines

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[edit] Enzyme/Compound Structures

Enzyme and compound structure images should have consistent presentation.

[edit] Compounds

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The presentation of compounds should be:

  • Skeletal structures (ie. 'joints' and not 'C's to represent carbons)
  • All carbon bound hydrogens should be ommited (unless demonstrating stereochemistry)
  • Steriochemistry should be indicated via 'wedge' and 'dashed' bonds
  • Approx 22 pixel long bonds and size 12 Arial lettering
  • .png format, anti aliased and well cropped
  • Named with the molecule name, with spaces replaced by hyphens ('-'), and with _wpmp added on the end to show compliance with these conditions (eg. alpha-D-glucose-6-phosphate_wpmp.png)

To produce compound images I personally use bkchem [1] to draw the structure (.svg), inkscape [2] to export to bitmap at 72dpi (.png) and the gimp [3] to crop. These programes are all free for non-commercial use.

[edit] Enzymes

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The presentation of enzymes should be:

  • 'Cartoon' structures
  • Show all subunits and any dimerisation/polymerisation
  • On a white background
  • Oriented to show symmetry and dimerisation clearly
  • .png format, and at least 300x300px, and preferably more

To produce enzyme images I personally use pymol [4] with the command 'ray 1024,1024' to produce large, anti aliased images. This program is free for non-commercial use.

For proteins which have important structural features, images which show the protein surface semi-transparently and the cartoon structure may be more appropriate. For example:


Cn3D [5] may be simpler to use. For more complex diagrams (eg. showing both the surface structure, cartoon structure and a cutaway) I am experimenting with BALL [6]. This is significantly slower than pymol or cn3d, but is more powerful.

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