Wikipedia:Manual of Style/Chemistry/Structure drawing

This is an explanatory essay about Wikipedia:Manual of Style/Chemistry.

This page provides additional information about concepts in the page(s) it supplements. This page is not one of Wikipedia's policies or guidelines as it has not been thoroughly vetted by the community.

Shortcuts

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

Chemical structures and reaction schemes should conform to the following:

Images should be drawn with a molecule editor, never freehand
ACS settings should be used for both structures and reaction schemes. These settings are normally available as templates in chemical drawing programs. Use sans-serif fonts like Arial.
Indexes used for labelling must be superscripted: R¹-CH₂-R² (not R₁-CH₂-R₂)
Do not include English text in images: this prevents their reuse in other languages.
Methyl groups should be denoted with “CH₃”, not “Me”, unless they are bound to a heteroatom (for example, “NMe₂”). This is to avoid confusion with “Me”, the German abbreviation for metal (Metall). The use of “Et”, “Pr”, etc., is discouraged. By default, “Ph” denotes phenyl and “X” halogen.
The use of explicit methyl groups in the following cases is a stylistic choice, and both forms are generally acceptable on Wikipedia:
- methyl groups attached to a ring or as branches in a longer carbon chain;
- methyl groups at the end of a carbon chain.
If labels for structures are desired, consider the use of bolded numerals, which are language-neutral.
Information about stereocenters and stereoisomerism should be included if available (e.g. by using wedged bonds).
For articles on racemates, the stereochemistry should be depicted as undefined (straight and not wavy nor wedged bonds attached to the stereogenic center).

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

Images should be uploaded in PNG or SVG format. PNG images should be around 600–720 dpi. A transparent background should be used. Images should still be readable when scaled down to 450 pixels to prevent conflicts with the Chembox.
SVG images are desirable because they are infinitely scalable, while remaining compact. However, support for SVG images among common molecule editors is limited, and may not be rendered correctly on Wikipedia.
Scanned images tend to be of poor quality. Scanned images of books or journals may violate copyright. Do not upload them.

Suggested molecule editor settings

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.

From the "Options" menu, choose "Set Structure Drawing Style" → ACS Style
Draw the structure or reaction diagram
Export the file as PNG or EMF for further processing (see below)

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..

From the "Options" menu, choose "Load Settings" → ACS document
Draw the structure or reaction diagram
Export the file as PNG or EMF for further processing (see below)

Drawing in ChemDraw

From the “File” menu, choose “Apply document settings from → ACS Document 1996”.
Draw the structure, and save it as a ChemDraw file.
If you drew the structure before applying any settings, then you need to select the object, open the “Object” menu and choose “Apply document settings from → ACS Document 1996”.
Then save it as a PNG file, to be read by an image editor such as GIMP or IrfanView (see below for details).

The ACS settings are as follows:

Chain angle: 120 degrees
Bond spacing: 18% of length
Bond length: 0.508 cm (14.4 pt)
Bold width: 0.071 cm (2 pt)
Line width: 0.021 cm (0.6 pt)
Margin width: 0.056 cm (1.6 pt)
Hash spacing: 0.088 cm (2.5 pt)
Captions: Arial 10 pt
Atom labels: Arial 10 pt
Bond angles and length: “fixed” is recommended

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)

Font: Arial
Font scale: 18
Carbon labels: Never (which may be done by going to Edit → Preferences → Structure)
View → Colors: Monochrome

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

Double bond spacing: 0.18
Wireframe bond thickness: 0.06
Circled charge labels font: Arial

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

Down wedge orientation: Points Upward (Daylight)

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

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

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

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

Draw the structure in ChemDraw 12 or later
Go to File → Save As
Choose Scalable Vector Graphics (*.svg) as the save as format.

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

Draw the structure in ChemDraw 12 or later
Go to File → Save As
Choose PDF as the save as format
Upload the resulting PDF to the Texterity FreeSVG converter and you should end up with a very light SVG.
Alternative free SVG converter: Online SVG converter.

Using MarvinSketch

Click File → Export to Image.
Change the filename extension to “.svg” or choose the file type Scalable Vector Graphics / SVG (*.svg *.svgz), and click Save.
Set the Scale value to 112.
Check the Use Alpha Channel box and, finally, click Save.

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).

Draw the structure in your molecule editor, and save it as a Windows Metafile (.wmf), Enhanced Metafile (.emf), or Encapsulated Postscript (.eps).
Open the saved file in Inkscape.
Resize the picture about 400%, then click to File→Document Properties→Fit page to selection.
Select the molecule and click Path→Object to path. (to workaround commons:librsvg bugs with fonts)
Click File→Save as to save file as Plain SVG.

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.

Draw the structure in your molecule editor (ideally change the settings to give a molecule twice the size as the JACS standard or change the size to 200% before next step), and save it as an Encapsulated PostScript file (.eps) - many of the Apple print drivers (an Apple printer is not required) that print to a PostScript printer can be set to EPS in the print dialog options, thus printing to a file generates an suitable EPS file (HP printers with PS in the name e.g. "HP LaserJet 2300 Series PS" also work - ideal for Windows 7 where Apple drivers are hard to find)
Open the PostScript file in Scribus. Note the image size and set the paper size to about 10px larger than the largest dimension.
- NB:SymyxDraw will usually add a full page rectangle to the drawing - ungroup, select rectangle and delete, then select all and re-group structure.
Go to File → Export → Save page as SVG.

Uploading and copyright

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:

Go to the upload page (you may want to bookmark this)
Paste this text to the summary template:

For ChemDraw:

{{Information
| Description= {{en|Chemical structure of [[:en:...|]]}}
| Source= {{Own}}
| Date= 2024-11-30
| 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= 2024-11-30
| 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]]

Replace the “...” with the Wikipedia article name and your username, respectively
The date is already set to the current date
Browse to your file and select it. Optionally, change the final image name in the box below
Do not select a licensing from the upload form — the tags are already in the pasted text
Upload the file
Change your structure to the most specific subcategory (or subcategories) of Category:Chemical compounds

Templates

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}}

This chemical structure or diagram's factual accuracy is disputed.

Page last edited 320 days ago

reason.

Please discuss the issue on this diagram's talk page.
See also: Wikipedia structure drawing guide.

Usage: {{Disputed chem|why}} – All: Category:Disputed chemical diagrams

Wikipedia: {{Low quality chem|reason}}

Commons: {{Low quality chem|reason}}

External links

Graphical Representation of Stereochemical Configuration IUPAC Recommendations 2006. A guide to drawing chemical structures. Covers topics such as the use of wedged and wavy bonds, bond angles, and perspective.

Notes