Avogadro, the Master Builder

Avogadro [8] does not aim to represent known structures, even though the application can do so; instead, you build your own molecule with Avogadro without having to know the coordinates of the individual atoms.

To begin, you just start to draw the rough structure from atom to atom. Then, you can start optimization mode and let Avogadro optimize the geometry of the molecule in line with energetic considerations: The lower the binding energy, the more dense the molecule is in the real structure. After composing the molecule, you then measure it and tell Avogadro to output the atom coordinates (Figure 5).

Figure 5: As a molecular builder, Avogadro not only lets you view molecules but also design them and output the atomic coordinates.

PyMOL, the All-Rounder

PyMOL's [9] capabilities are demonstrated in Figure 2; the program computes and shows the electron density incrementally in line with the instructions [2]. PyMOL is as complex as it is powerful and consists of a script window and an image window, where it shows the computed image.

If you load multiple images, such as the molecule and the electron density space, as in Figure 2, then you can label the individual views by using the buttons labeled to the right of the image window. In my experience, masterful use of the PyMOL program is unlikely to be achieved without occasionally referring to the manual [10] – performance has its price.

GChemPaint, the Outsider

Strictly speaking, GChemPaint [11] is not in fact a visualization program. It made its way into our lab by virtue of one neat property: It can read data in the popular PDB molecule format of the Protein Data Bank [12], a freely accessible database that contains resources contributed by international biologists and biochemists in the form of 3D structures of proteins and nucleic acids.

The GChemPaint program shows the structural formula directly from the PDB coordinate files. This structural formula is then more useful in scientific documentation than a 3D visualization – as long as the molecules are not too big (Figure 6).

Figure 6: GChemPaint converts PDB files into structural formulas, which are better suited for scientific publications – at least for simple molecules.