Wikipedia:Wikiproject Metabolic Pathways/style guidelines

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Contents 1 Enzyme/Compound Structures 1.1 Compounds 1.2 Enzymes 1.2.1 Pymol

[edit] Enzyme/Compound Structures

Enzyme and compound structure images should have consistent presentation.

[edit] Compounds

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

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

[edit] Pymol

To produce enzyme images I reccomend use PyMol [4] 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.