visualization. While small molecules are easy to visualize,
large molecules of thousands of atoms or more are more
difficult. Thus, we mainly focus on how to visualize large
molecules. At the end of Section ‘‘Protein visualization’’,
we will give results obtained via GridMol.
GridMol reads files of many different formats (see
Fig. 3) through factory design patterns, enabling easy
addition of novel formats. GridMol can currently read files
of types of pdb, Gaussian Com, Gaussian Log, Gaussian
Gjf and xyz format. Additional file formats can be read by
adding a new reading pattern.
Three-dimensional representation of molecules
There are many kinds of representations for the same
molecule. Different representations highlight different
aspects of the molecule, each having unique advantages
and disadvantages. GridMol has different display models,
listed below (Note: all the pictures are generated by
GridMol).
Line Model (Fig. 4). Bonds are shown as lines while
atoms are not displayed. This model clearly represents
those connections between all atoms.
Ball-and-stick model (See Fig. 5). All atoms are shown
as spheres of different size and all bonds are as cylinders of
different length. This model is clear for understanding
molecule structure. However, it leads to slow rendering and
thus user interaction due to larger memory load than other
models, such as the line and tube models.
Space-filling model (Fig. 6). All atoms are shown as
spheres of different size and different color according to
their van der Waals radius and atom types while bonds are
Fig. 3 GridMol scalable file reading design
Fig. 4 Line model (PDB ID: DICK)
Fig. 5 Ball-and-stick model (PDB ID: DICK)
J Comput Aided Mol Des (2008) 22:119–129 121
123
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