User:Benjah-bmm27/MakingMolecules

Making molecules

Here's how I make molecular models for Wikipedia:

• Learn enough chemistry and crystallography to be able to make images that accurately portray chemical structures reported in the scientific literature. This is not trivial. Ask at WT:CHEM for advice if you're new to this.
• Get a molecule editor. I use Avogadro and/or CCDC Mercury.
• Find a literature structure, typically determined by crystallography (single crystal or powder, X-ray, neutron or occasionally electron diffraction). Try the Cambridge Structural Database for organics and organometallics (e.g. via this form), Crystallography Open Database for all kinds of substance (here), AMCSD for minerals or the Inorganic Crystal Structure Database for inorganics. Many ICSD entries now appear in the CSD, although finding them can be tricky. Try using the DOI of your literature reference. For simple molecules in the gas phase, you may be able to find structural parameters from the microwave spectroscopy, infrared spectroscopy or gas electron diffraction literature.
• Ideally, read a bit about the substance and its structure in a secondary source such as a review article or textbook. Greenwood & Earnshaw's Chemistry of the Elements, A. F. Wells's Structural Inorganic Chemistry, Housecroft's Inorganic Chemistry and March's Advanced Organic Chemistry are good choices.
• Orient the molecule in the way you'd like it to appear in your final image
• Choose a style in which to render your molecule. Typical options include space-filling / CPK / van der Waals radii, ball-and-stick, stick, polyhedra or wireframe.
• Check what you see in front of you is how you want the completed image to look
• Export to PNG (larger than you intend the final Wikipedia image to be, say 4000 pixels longest side)
• Edit the image in, for example, Photoshop
• Crop the image then re-add a border to the top, bottom, left and right sides - typically 10% of longest side, so
• Resize the image to something sensible for Wikipedia - I usually make the longest side of the image 3000 pixels. This is better than saving the image to 3000px width directly from the molecular graphics app because it makes for a smoother, antialiased image.
• Export from your image editing app as a high-quality PNG and upload it to Wikimedia Commons. I use the old form and add a comprehensive image description, with a link to the literature, details of which software I used to produce the image and a colour key.
• Add your image to an article, either in the chembox, as a thumbnail image or in a gallery. It is often helpful to add the literature reference to the image caption as well as the image description page, so readers can see it is referenced without having to click on the image.

Hope this helps

Archived

Old advice for Discovery Studio Visualizer is here.