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International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 25.2, pp. 725-726
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The basic model for the execution of MolScript is that of a non-interactive image-creating script processor. There are two stages in the execution. First, the script is parsed and the graphics objects are created according to the commands. This stage is essentially independent of the output format. Second, when the end of the script has been reached, the image is rendered from the graphics objects according to the chosen output format.
The viewpoint in the MolScript right-handed coordinate system is always located on the positive z axis, looking towards the origin, with the positive x axis to the right. The user obtains the desired view of the structure by specifying rotations and translations of the atomic coordinates; it is not possible to change the location or the direction of the viewpoint.
There are two main benefits with this scheme: The first is that it is similar to the way we handle objects in everyday life: we do not normally fly around the object, but rather move it about with our hands. The other benefit is that together with the coordinate copy feature it can be used to compose an image containing several geometrically related subunits.
The disadvantage is that the atomic coordinates must be transformed before the creation of the graphics objects. This may complicate the composition of an image where another structure or geometric object is to be included. For example, if two separate structures have been aligned structurally by some external procedure, then the user must take care not to destroy the alignment in the process of setting the viewing transformation.
The graphics state consists of the parameters that determine the exact visual appearance of the graphics objects. The default values of the graphics state parameters are reasonable, so that an image of acceptable quality can be produced quickly. However, to obtain high-quality images which emphasize the relevant structural features, the user must usually fine-tune the rendering by modifying the graphics state parameters appropriately for the various graphics objects.
The graphics state may be modified by using the `set' command at any point in the script file. The change can have an effect only on graphics commands below that point in the script. When a graphics command is processed, the object is created according to the current values of the graphics state parameters at that exact point in the script file. It is this property of the graphics state that gives the user a very high degree of control over the composition and appearance of the graphics objects.
A new feature in version 2 of MolScript is the ability to set the colour of residues on a residue-by-residue basis in schematic secondary-structure representations. It is also possible to set the colour of atoms and residues according to a linear function of the B factors.
The graphics commands create the graphics objects to be rendered in the final image. The commands need an atom or residue selection (see below) as argument. The visual attributes, and in some cases the dimensions, of the objects are determined by the graphics state parameters.
The graphics objects include the most common ways to represent atoms, such as simple line drawings, ball-and-stick models and CPK (Corey–Pauling–Koltun) spheres approximating the van der Waals radii of the atoms. The graphics objects representing high-level structures are mainly designed for protein structures, and comprise arrows for β-sheet strands, cylinders or helical ribbons for α-helices, and coils for non-repetitive peptide chain structures. The coil object can also be used to represent oligonucleotide backbone structures.
A set of basic atom and residue selections are provided in MolScript for use as arguments to the graphics commands. Arbitrary subsets of atoms or residues can be specified by joining together the basic selections using a form of Boolean operators. Unfortunately, the Boolean expression feature may sometimes be difficult to understand for the non-expert user. One should consider the entire expression as a test to be applied to every atom or residue. Any atom or residue for which the Boolean expression evaluates to `true' will be selected as argument for the command.
Externally defined objects described by points, lines or triangular surfaces may be included in the image. The objects may optionally be transformed by the most recent transformation applied to the coordinate data. This feature allows import of arbitrary geometry created by some external software, e.g. molecular surfaces, electron-density representations or electrostatic field lines. The graphics state parameters apply to the rendering of the external objects in the image.
