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Sample molecular drawing

Software I like: BKChem

BKChem is a 2-D tool for drawing chemical structures.


These notes are from 2009 May. As of 2014 Oct 10, the latest releases (according to Wikipedia) are from 2009 Feb 23 (stable) and 2010 Aug 12 (preview), and the project Web site does not respond.


This is a very brief introduction to a few of the tools, based on my very limited experience, just to get a new user started. For more details see the user's manual in the doc/html/ directory installed with BKChem, and other documentation on the BKChem wiki.

The mode-selection panel is shown at the right.

Draw tool To draw a chemical structure, click on the draw tool and then click in the drawing area. A line will appear. Click on one end of the line and a connected line will appear. To control the orientation when creating a new line, click and drag in the desired direction. Click in the middle of a line to change it to a double or triple line. There are also tools for adding standard templates, user-defined templates, arrows, etc.

Atom tool To add or edit a node label, click on the atom tool and then click on the node. The text-entry area will become active. Enter the desired node label and hit the Enter key. Some text strings will be recognized and interpreted as element names; for example, ‘h’ or ‘H’ will be interpreted as hydrogen. The labels for carbon atoms are not displayed; there is an option to not display hydrogen labels but I haven't got it to work. There are also tools for marking atoms with electrons, orbitals, etc.

Text tool To add or edit text, click on the text tool and then click in the drawing area where the text is to appear. The text-entry area will become active. Enter the desired text and hit the Enter key. Some special formatting is possible, such as bold and italics. New lines can be indicated using \n but this seems to cause problems with subsequent editing and is not well supported for display outside BKChem.

Edit tool To select objects for moving or deleting, click on the edit tool. Select an object by clicking on it. Select multiple objects by using shift-click or by clicking and dragging to surround the objects with a selection rectangle. Move selected objects by clicking and dragging. The Align menu contains tools for aligning objects horizontally and vertically. Delete selected objects by using the Delete or Backspace keys.

Displaying on the Web

The native file format is a form of SVG. Two somewhat different SVG formats are also exported, and two flavours of PDF are exported. My experience (very limited) is that the most successful method is to just use the native SVG file for display in Firefox. BKChem uses \n to specify new lines in text but the new lines are respected only in one of the PDF formats, and that format had other problems with my example. The \n also seemed to cause problems when editing text so it may be best to avoid it altogether.

R. Funnell
Last modified: 2014-10-10 07:47:47