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Manual of Style for Chemical Structure Drawing

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Chemical structure(s) on this Wiki are provided in every article devoted to a small-molecule drug. Previously only a single two-dimensional (2D) structure in the drugbox was required, now three-dimensional (3D) structures are also required in their own respective section.

Required structuresEdit

Required structures for a non-chiral, non-cis/trans-isomeric or single-isomer small molecule drug include:

  • 2D structure, which is included in the Help:Drugbox
  • Static 3D structure, at least one of which should be in the drugbox.
  • Animated 3D GIF format structure.

As for chiral or cis/trans-isomeric drugs with more than one isomer included in the product the drug article is on then the following structures are required:

  • 2D structure of the two isomers; a generalized structure (showing no isomerism, e.g., File:Venlafaxine.svg vs. File:Venlafaxine_racemate.svg) can be used in the drugbox, but the two isomers must appear in 2D somewhere in the structure.
  • Static 3D structure of both isomers.
  • Animated 3D GIF structures of the two isomers.

Style guide for drawing 2D structuresEdit

Generally the ACS style is preferred, see the corresponding Wikipedia style guide (1) for different ways to do this. These structures must be skeletal formulas, that is, drawn using line-angle notation. All structures must be drawn electronically, not by hand, so as to ensure consistency and eligibility. They cannot be subject to copyright[note 1] aside from under the CC-BY-SA 3.0 license or equivalent.

Additionally a few extra conditions are required to be satisfied by 2D structures uploaded to this Wiki:

An example of an invalid structure
Fluoxetine incorrect
Incorrect fluoxetine structure with incorrect portions boxed
For example, H should appear above the nitrogen in the amine group; the CH3 should be left implicit in the skeletal formula and the CF3 should be drawn in skeletal formula format too.
  • They must be cropped, with no visually obvious spaces between the structure and the sides of the structure.
  • They must be in SVG format.
  • Backgrounds must be transparent.
  • The structure must be monochromatic, that is, in black and white.
  • C should never appear in the structure, rather they should be replaced by line-angle notation. For example, CF3 groups should be drawn in full form, that is the fluorine atoms (F) coming out, single-bonded to the central carbon (that is not denoted by a C label). Likewise methyl groups should always be drawn like the N-methyl (i.e., the one coming off the amine NH group) group is in this file.
  • Amine groups should be drawn in the way that produces the least crowding or overlap with bond lines (see the diagram to the right).

Drawing guides for specific pieces of softwareEdit

Style guide for 3D structure drawingEdit

General requirements for 3D structures include:

  • They use CPK colours (e.g. see [1]), this [2] palette is also acceptable. Carbons should preferably be black, although grey is also acceptable.
  • They are based on crystal structures or NMR structures,[note 2] although if these structures are unavailable PubChem SDF files with optimization of these structures, especially in Avogadro, is preferred. In Avogadro the keyboard shortcut, Ctrl+Alt+O may be used to optimize a structure's geometry.
  • Backgrounds must be either white or transparent, with a preference for transparent structures, although for animated GIF files this can be quite difficult to achieve.
  • They should be cropped (removing unused space) to the greatest extent possible. For animated GIFs this may be difficult to achieve, but it usually can be achieved if the GIF is created in GIMP.

Static structuresEdit

Note: see Help:Chemical structure drawing/Accelrys Discovery Studio Visualizer, for how to create a static 3D model fulfilling these requirements using Accelrys DS Visualizer.

Sertraline3D

Sertraline's 2D structure

Static structures may be produced using Accelrys DS Visualizer, Avogadro, Jmol or other pieces of software. There are a number of additional requirements that need to be imposed on these structures:

  • They should display as much detail of the molecule's 3D structure as possible for a static diagram.
  • Aromatic rings should be displayed with a delocalized charge across the ring. For example, see the structure of sertraline to the right.
  • Backgrounds must be transparent.
  • Models must be in ball and stick format.
  • They should be in PNG or SVG format. PNGs are often preferable as vectorization causes some loss of quality. 




Animated GIF filesEdit

Animated GIF files are GIF files consisting of several frames animated in a sequence. They can be created using several pieces of software with Jmol and PyMOL being the most notable free examples of such software. These files can be produced directly from a 3D molecular modelling software or from a sequence of PNG or JPG snapshots taken at constant angles from each other using an image-manipulation software like GIMPJmol is capable of directly producing animated GIFs itself, but frequently Jmol structures uploaded to this Wiki have been animated using GIMP. PyMOL is not capable of producing animated GIFs by itself, and rather the sequence method must be used. 

NotesEdit

  1. Ruling out structures that are scanned or copy-pasting from textbooks (print or electronic) or journal articles.
  2. For small molecules searching crystallography.net is usually the most efficient free way to find these structures. It is worth noting, however, that the English Wikipedia often has small-molecule crystal structures drawn by Ben Mills on their pages and if you find the paper he is citing and view it yourself then it may be possible to create a crystallographic information file [CIF] yourself. See Help:Chemical structure drawing/Creating CIFs from raw data for details as to how to do this. Structure data on large molecules (e.g., proteins and strands of DNA) can be found in the wwPDB databases such as RCSB PDB and PDBe. These structures often also contain the structure of small-molecule ligands, and these are also acceptable sources for the structure of small molecules.

See alsoEdit

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