View source for Wiki143:Manual of Style/Chemistry/Structure drawing

{{Supplement|interprets=Wikipedia:Manual of Style/Chemistry|MOS:CSDG|MOS:CHEM/Structure|WP:Chem/Structures|MOS:Structure drawing}}
{{MOSCHEM}}
These guidelines are necessarily quite technical, and are intended for editors with some experience of drawing [[structural formula]]e 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
* [[American Chemical Society|ACS]] settings should be used for both structures and reaction schemes. These settings are normally available as templates in [[molecule editor|chemical drawing programs]]. Use ''sans-serif'' fonts like Arial.
* Indexes used for labelling must be superscripted: R<sup>1</sup>-CH<sub>2</sub>-R<sup>2</sup> (not R<sub>1</sub>-CH<sub>2</sub>-R<sub>2</sub>)
* Do not include English text in images: this prevents their reuse in other languages.
* Methyl groups should be denoted with "CH<sub>3</sub>", not "Me", unless they are bound to a heteroatom (for example, "NMe<sub>2</sub>"). 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 [[stereocenter]]s 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 ({{Color box|#ffff30}}) 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|PNG]] or [[.SVG|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 [[Template:Chembox|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 render 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 [[molecule editor|chemical drawing programs]].

===Drawing in ACD/Chemsketch===
[[ACD/ChemSketch]] is freeware available for personal, home, and educational use from [https://www.acdlabs.com/resources/free-chemistry-software-apps/chemsketch-freeware/ 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 [https://discover.3ds.com/biovia-draw-academic 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===
The free, open-source program called WinDrawChem (the Windows version of [[XDrawChem]]) appears to work well. ([https://sourceforge.net/projects/xdrawchem/ 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 &rarr; 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]] ([https://bkchem.zirael.org/ link]). You can save the following configuration files to <tt>~/.bkchem</tt> under Linux or <tt>C:\Documents and Settings\{username}\application data\bkchem</tt> ([[Windows XP|XP]]) or <tt>C:\Users\{username}\application data\bkchem</tt> ([[Windows Vista|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:
<syntaxhighlight lang="xml">
<?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>
</syntaxhighlight>

prefs.xml:
<syntaxhighlight lang="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>
</syntaxhighlight>

==3D Models==

===CORINA online===
[https://mn-am.com/products/ 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==
[[Scalable Vector Graphics|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.
<small>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.</small>

===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 [http://freesvg.texterity.com:90/ FreeSVG] converter and you should end up with a very light SVG.<!-- gone? moved? many things re-used the name FreeSVG / Free SVG. -->
* Alternative free SVG converter: [http://image.online-convert.com/convert-to-svg 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 [[WP:SUL|single user login]], you might already have an account on Commons ([[Special:MergeAccount|check here]]).

As usual, '''uploaded images must have a correct copyright tag:''' please add {{template link|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 '''[[Commons:Commons:Upload/Chemistry|this pre-filled upload form]]'''. Please complete the form and one or more specific categories (normally subcategories of [[Commons:Category:Chemical compounds|Category:Chemical compounds]]).

Alternative method:
* Go to the [http://commons.wikimedia.org/w/index.php?title=Special:Upload&uploadformstyle=basic upload page] (you may want to bookmark this)
* Paste this text to the summary template:
: For ChemDraw:
 <nowiki>{{Information</nowiki>
 <nowiki>| Description= {{en|Chemical structure of [[:en:...|]]}}</nowiki>
 <nowiki>| Source= {{Own}}</nowiki>
 <nowiki>| Date= </nowiki>{{CURRENTYEAR}}-{{CURRENTMONTH}}-{{CURRENTDAY}}
 <nowiki>| Author= ~~~</nowiki>
 <nowiki>| Permission= {{PD-chem}}</nowiki><!--or {{PD-self}}-->
 <nowiki>| other_versions=</nowiki>
 <nowiki>}}</nowiki>
 <nowiki></nowiki>
 <nowiki>==Comments==</nowiki>
 <nowiki>High-resolution black/white .PNG made with [[:en:ChemDraw|ChemDraw]] and [[:en:IrfanView|IrfanView]] &mdash; 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.</nowiki>
 <nowiki></nowiki>
 <nowiki>[[Category:Chemical structures]]</nowiki>
: For BKchem:
 <nowiki>{{Information</nowiki>
 <nowiki>| Description= {{en|Chemical structure of [[:en:...|]]}}</nowiki>
 <nowiki>| Source= {{Own}}</nowiki>
 <nowiki>| Date= </nowiki>{{CURRENTYEAR}}-{{CURRENTMONTH}}-{{CURRENTDAY}}
 <nowiki>| Author= ~~~</nowiki>
 <nowiki>| Permission= {{PD-chem}}</nowiki><!--or {{PD-self}}-->
 <nowiki>| other_versions=</nowiki>
 <nowiki>}}</nowiki>
 <nowiki></nowiki>
 <nowiki>==Comments==</nowiki>
 <nowiki>CD-SVG file made with [[:en:BKchem|]] — see [[:en:Wikipedia:Manual of Style (chemistry)/Structure drawing|WikiProject Chemistry - structure drawing]] for detailed instructions.</nowiki>
 <nowiki></nowiki>
 <nowiki>[[Category:Chemical structures]]</nowiki>
* 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 [[Commons:Category:Chemical compounds|Category:Chemical compounds]]

==Templates==
The following templates can be used on Wikipedia and [[Wikimedia Commons|Commons]] to mark wrong or poor chemical structures:
{| width="100%"
|-
| Wikipedia: [[Template:Disputed chem|<nowiki>{{Disputed chem|reason}}</nowiki>]]
Commons: [[Commons:Template:Disputed chem|<nowiki>{{Disputed chem|reason}}</nowiki>]]
| {{Disputed chem|reason}}
|-
| Wikipedia: [[Template:Low quality chem|<nowiki>{{Low quality chem|reason}}</nowiki>]]
Commons: [[Commons:Template:Low quality chem|<nowiki>{{Low quality chem|reason}}</nowiki>]]
| {{Low quality chem|reason}}
|-
|}

==See also==
* [[Wikipedia:Preparing images for upload]]
* [[User:Benjah-bmm27/MakingMolecules]]

==External links==
* [https://publications.iupac.org/pac/2006/pdf/7810x1897.pdf 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==
{{Reflist}}

[[Category:Wikipedia essays and information pages about the Manual of Style]]
[[Category:Wikipedia Manual of Style (chemistry)|Structure drawing]]