2. Creating a molecule scheme with bkchem

The best application i found for creating a molecule scheme is bkchem. It has an excellent user interface for scheme edition and reads smiles¹ files.

In comparison with other applications, i found bkchem has very practical and friendly tools for performing edition operations, where the others becomes very annoying and even impossible.

Let's introduce the user interface of bkchem by creating the scheme of D-glucose molecule (the figure is what we want to obtain as final result)

1. Go to main menu -> Chemistry -> Read SMILES and enter the smiles string for D-glucose O=C[C@H](O)[C@@H](O)[C@H](O)[C@H](O)C(O).
2. Select the "transformation mode" set of tools (from the first line of icons menu), and using its different tools unfold and align the obtained structure.
3. In order to fix the group symbols order (in our example, OH instead of HO, or viceversa) click right button over the group, and select option Symbol positioning. Select center last or center first, according to your needs.
4. Finally lets fix the bond draws in order to reflect the correct stereo isomer configuration. Use the "draw" set of tools and fix bonds with the wedge and hatch tools.
5. bkchem saves the image directly in SVG (Scalable Vector Graphics) format, another big advantage i found with this program. SVG graphic format is very suitable for edition of molecule schemes, because is based on vector primitives instead of pixels. And most important browsers and document editing applications supports it. Before saving the file, just ensure to crop the image to the area of the scheme (main menu -> File -> File properties) with a nice margin.

This has been an introduction using just a small subset --but the most used-- of tools among all the possibilities this application provides, so i leave for you the task for exploring the rest.

Notes

[1] On smiles files, see previous post, Visualizing a 3D structure of a molecule with jmol.