Wikipedia:WikiProject Molecular and Cell Biology/Metabolic Pathways task force/style guidelines
Enzyme and compound structure images should have consistent presentation.
The presentation of compounds should be:
- Skeletal structures (ie. 'joints' and not 'C's to represent carbons)
- All carbon bound hydrogens should be omitted (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  to draw the structure (.svg), inkscape  to export to bitmap at 72dpi (.png) and the gimp  to crop. These programmes are all free for non-commercial use.
The presentation of enzymes should be:
- 'Cartoon' structures
- Show all subunits and any dimerisation/polymerisation
- On a white or transparent background
- Oriented to show symmetry and dimerisation clearly (easy) or the active site and substrate/product binding (for detail in the article).
- .png format, and at least 300x300px, and preferably more
- Download the appropriate ".pdb" file from PDB.
- Open with PyMol.
- Set the background colour to white: Display>Background>White
- Set the background to transparent: Display>Background>Opaque
- Display the protein as cartoon structure either using the side bar of the display window, or by using the following script in the command line:
- hide everything, all
- show cartoon, all
- Rotate the protein using the left mouse button to click and drag. It is often possible to simply use PyMol to automatically orientate it; use the script:
- Render a nice, high quality image for wikipedia. This can either be ray traced (slower but prettier) or Direct3D rendered (much faster but uglier). Be warned, a complex protein may have a ray trace render time of around 10 mins. Use the command:
- ray 1620,1620
- draw 1620,1620
- ray 1620,1620
For proteins which have important structural features, images which show the protein surface semi-transparently and the cartoon structure may be more appropriate. See right for an example.