Wikipedia:WikiProject Molecular Biology/Metabolic Pathways task force/style guidelines

Enzyme/Compound Structures
Enzyme and compound structure images should have consistent presentation.

Compounds
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.

Enzymes
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

Pymol
To produce enzyme images I recommend use PyMol with the command 'ray 1024,1024' to produce large, anti aliased images. This program is free for non-commercial use.


 * 1) Download the appropriate ".pdb" file from PDB.
 * 2) Open with PyMol.
 * 3) Set the background colour to white: Display>Background>White
 * 4) Set the background to transparent: Display>Background>Opaque
 * 5) 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


 * 1) 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:
 * orient


 * 1) 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
 * or
 * draw 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.