Drawing 2D Molecules in Linux
Some people like to see 2D stick diagram models of molecules, such as the Windows program ChemDraw produces. An old page describes the use of XDrawChem and BKChem. However, a more modern solution is Marvin Sketch, as described here. Marvin is written in Java, so runs well on Linux, MacOS and Windows. It is a commercial product, produced by ChemAxon, but the version we have installed is distributed at no cost, and has considerable functionality.
As before, this page describes how to use the program to draw one simple molecule. The product is capable of rather more. As before, the example molecule is trinitrotoluene.
msketch
First select the aromatic 6-membered ring (bottom, second from right), then click somewhere on the canvas.
Then select the bond tool (top of column at left-hand side of canvas), and click on the four sites to which groups should be added. Marvin will default to assuming that carbon should be added, and add extra hydrogens automatically, so one ends up with four methyl groups, one of which was actually wanted!
Then from the menus choose Insert, Groups, click on the small circle in front of the N, the small circle in front of the NO, and finally on NO2 and click close. The mouse cursor will now have an NO2 group attached to it. Simply click on the three methyls which need changing.
Output formats include PostScript (File, Print, Print to File), PDF (File, Save As, PDF), and PNG (File, Export to Image). There seems to be no EPS option, and the PDF option lacks some characters in this example. The PS option turns the letters in the chemical groups into lines, rather than keeping them as text, which is odd.
Of course, structures one wishes to reuse should be saved in Marvin's own mrv format.
Comments / corrections to mjr19 at the obvious University (not Departmental) domain.