Manual of Style
Chemistry
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These guidelines are necessarily quite technical, and are intended for editors with some experience of drawing chemical structure diagrams and reaction schemes. For a less technical overview of the issues involved, see Wikipedia:Molecular structure diagram.

General[edit]

Chemical structures and reaction schemes should conform to the following:

Use of color

It is not necessary to color-code atoms according to element in structure drawings but if done the conventions of the Jmol scheme should be used. Note, however, that the use of yellow ( ) for sulfur is not advised as it can cause accessibility problems on a white background. Within a given article, diagrams should be consistent, which means in most cases they should use black and white except as highlighting to emphasize a particular point in specific diagrams. In all cases the advice at WP:color should be followed.

Technical considerations[edit]

Suggested molecule editor settings[edit]

ACS templates are available in most chemical drawing programs.

Drawing in ACD/Chemsketch

ACD/ChemSketch is freeware available for personal, home, and educational use from ACDlabs. It has comprehensive chemical drawing features and can directly connect to PubChem, eMolecules and Chemspider to search these large databases by structure or substructure. The program can read and write in many file formats including export of PNG files. If SVG files are required, it is recommended that structure diagrams be exported as enhanced metafiles (.emf) which can be read by Inkscape and other image editors.

Drawing in Biovia Draw

BIOVIA Draw is the current version of the original ISIS/Draw program, now owned by Dassault Systèmes and freely available for academic and non-commercial users from BIOVIA. Other previous versions were called Accelrys Draw and SymyxDraw. The program can read and write many file formats, other than its proprietary sketch file format (.skc) and can export PNG files. If SVG files are required, it is recommended that structure diagrams be exported as enhanced metafiles (.emf) which can be read by Inkscape and other image editors..

Drawing in ChemDraw

The ACS settings are as follows:

Also recommended: For minus symbols on atoms, change the font for the minus symbol to “Symbol” for clarity.

Drawing in MarvinSketch

The following two changes in font may be performed by going to File → Document Style)

The following three may be performed by going to Edit → Preferences → Display:

Whereas this last one may be performed by going to Edit → Preferences → Bonds

Stereocenter display may be enabled by choosing View → Stereo → R/S Labels: All.

Drawing with WinDrawChem/XDrawChem

There is a free, open source program called WinDrawChem (the Windows version of XDrawChem) that appears to work well. Link. Unix-like users should follow the XDrawChem article link.

The configuration is extremely limited and post-processing is likely required. The only useful thing in "Format → Drawing settings..." is "Double bond spacing", which should be set to 18% of bond length, i.e. 5 pixels (integers only!) for the default 25-pixel bonds. Actual pixel sizes don't matter considering we will be doing an SVG report.

Drawing in BKChem

There is a free, open source program called BKchem (link). You can save the following configuration files to ~/.bkchem under Linux or C:\Documents and Settings\{username}\application data\bkchem (XP) or C:\Users\{username}\application data\bkchem (Vista / Windows 7) to get configuration according to Wikipedia's Manual of Style. It should work on any system with Python 2 and Tcl/Tk.

standard.cdml: 

<?xml version="1.0" ?>
<cdml version="0.15" xmlns="http://www.freesoftware.fsf.org/bkchem/cdml">
  <info>
    <author_program version="0.12.2">BKchem</author_program>
  </info>
  <standard area_color="" font_family="Arial" font_size="24" line_color="#000" line_width="0.06cm" paper_crop_margin="5" paper_crop_svg="1" paper_orientation="portrait" paper_type="Legal">
    <bond double-ratio="0.85" length="1.4cm" wedge-width="0.18cm" width="0.21cm"/>
    <arrow length="1.6cm"/>
  </standard>
</cdml>

prefs.xml : 

<?xml version="1.0" ?>
    <bkchem-prefs>
        <lang type="StringType">en</lang>
        <geometry type="StringType">1016x522+4+27</geometry>
        <recent-file1 type="StringType"></recent-file1>
        <recent-file2 type="StringType"></recent-file2>
        <use_real_minus type="IntType">0</use_real_minus>
        <default-dir type="StringType">~</default-dir>
    </bkchem-prefs>

3D Models[edit]

CORINA online

CORINA online is an easy to handle 3D-model generator of molecules, with the objective to execute the structural determination within a particular low time investment. This advantage is bought by a divergence from the ideal geometry. For instance, the program works with presets. To which extent these divergences are tolerable depends on the individual case and on quality demands. CORINA is not “foolproof”. Pseudochirality centers may turn out as pitfalls (e.g. amines that are chiral in protonated form). These specifics are to be considered in the SMILES code, i.e. the correct relative energy minimum is to be manually assured.

Generating PNG files[edit]

Most molecule editors cannot produce .PNG images directly with the requirements outlined above. The image processing step also allows a canvas (margin) to be added (this is usually absent from the molecule editor output).

  • Save as: TIFF black/white bitmap with a resolution of 720 dpi (small molecules) to 240 dpi (large molecules) (in ChemDraw under the Options button in the Save as TIFF dialog).
ChemDraw / ChemBioDraw 11 (2007) cannot save black and white TIFF images. Therefore, save as a 1200 dpi greyscale TIFF image and decrease the color depth to 2 bit (black and white) during image processing.
Image processing (Photoshop or Irfan view):
  • Add canvas of about 5% to each side (test it, usually around 30 pixels) (Photoshop: Image:Canvas Size, relative, 10% width, 10% height)
  • Save as a PNG black/white bitmap (color depth: 2) with transparent background.

Generating SVG files[edit]

SVG files are preferred, because they are smaller in filesize, can generate high quality images for printing and are easier to translate if text is added to mechanism.

Using ChemDraw 12 for Windows

ChemDraw exports svgs with a white background. You may use the vbs script at User:Smallman12q/Scripts/Transperify to make the background transparent. Another option is to open the file with Inkscape, right-click on the structure and select "Ungroup", then click anywhere on the white background and hit delete, then save again.

Using ChemDraw 12 for Mac

Using MarvinSketch

There tends to be an unreasonably large margin left around the diagram's extents, so it is often a good idea to crop the image in a vector program such as Inkscape before uploading it. Leave a small margin of 1.6 pt.

Using Inkscape

This method works only if your molecule editor is able to export files in Windows Metafile format. For example, ChemDraw supports this, as does ChemSketch and BIOVIA Draw (.emf is preferable for the latter).

Using Scribus

Alternative (but little more complex) way to generate high quality and small size SVG files. One needs to download and install both Scribus and Ghostscript to archieve EPS to SVG conversion.

Uploading and copyright[edit]

Please upload images to Wikimedia Commons and not to the English Wikipedia. This enables images to be used in other Wikipedia languages and other Wikimedia projects and makes updating images much easier, it also saves someone else having to move the structure to Commons later. It is also simpler to find images in the Commons category structure compared to Wikipedia. To upload images to the Commons, you must be a registered user there. Due to the single user login, you might already have an account on Commons (check here).

As usual, uploaded images must have a correct copyright tag: please add ((PD-chem)) - this will add the text This image of a simple structural formula is ineligible for copyright and therefore in the public domain, because it consists entirely of information that is common property and contains no original authorship. Images released under “non-commercial use only” licences are not accepted and will be deleted without warning, as will images without a tag.

The easiest way is to use this pre-filled upload form. Please complete the form and one or more specific categories (normally subcategories of Category:Chemical compounds).

Alternative method:

For ChemDraw:
((Information
| Description= ((en|Chemical structure of [[:en:...|]]))
| Source= ((Own))
| Date= 2024-04-17
| Author= ~~~
| Permission= ((PD-chem))
| other_versions=
))

== Comments ==

High-resolution black/white .PNG made with [[:en:ChemDraw|ChemDraw]] and [[:en:IrfanView|IrfanView]] — see [[:en:Wikipedia:Manual of Style (chemistry)/Structure drawing|WikiProject Chemistry - structure drawing]] for detailed instructions. Please drop me a note if you need the source file.

[[Category:Chemical structures]]
For BKchem:
((Information
| Description= ((en|Chemical structure of [[:en:...|]]))
| Source= ((Own))
| Date= 2024-04-17
| Author= ~~~
| Permission= ((PD-chem))
| other_versions=
))

== Comments ==

CD-SVG file made with [[:en:BKchem|]] — see [[:en:Wikipedia:Manual of Style (chemistry)/Structure drawing|WikiProject Chemistry - structure drawing]] for detailed instructions.

[[Category:Chemical structures]]

Templates[edit]

The following templates can be used on Wikipedia and Commons to mark wrong or poor chemical structures:

Wikipedia: ((Disputed chem|reason))

Commons: ((Disputed chem|reason))

Wikipedia: ((Low quality chem|reason))

Commons: ((Low quality chem|reason))

See also[edit]

External links[edit]

Notes[edit]

Categories