Rendering methods

All of the different rendering methods have various parameters which determine how they are drawn. For each method, there are controls in the Graphics window which modify the associated parameters, such as the line width and sphere resolution (the graphical controls are described in section 5.4.7). Table 6.1 lists the available rendering methods, and the following sections describe these methods and the parameters which modify their appearance.

Table 6.1: Molecular view representation styles.

Representation styles	Description
Lines	simple lines for bonds, points for atoms
Bonds	lighted cylinders for bonds
DynamicBonds	dynamically calculated distance-based bonds
HBonds	display hydrogen bonds
Points	just points for atoms, no bonds
VDW	solid van der Waal spheres for atoms, no bonds
CPK	scaled VDW spheres, with cylinders for bonds
Licorice	spheres for atoms, cylinders for bonds, same radius
Polyhedra	polyhedra connecting atoms within a cutoff radius
Trace	connected cylindrical segments through C${}_\alpha$ atoms
Tube	smooth cylindrical tube through the C${}_\alpha$ atoms
Ribbons	flat ribbon through the C${}_\alpha$ atoms
NewRibbons	smooth ribbon through the C${}_\alpha$ atoms
Cartoon	cartoon diagram (cylinders and ribbons) based on secondary structure
NewCartoon	smooth cartoon diagram (smooth ribbons) based on secondary structure
PaperChain	display ring structures as polygons, colored by ring pucker
Twister	flat ribbon tracing glycosidic bonds, with twists oriented by sugar residues
QuickSurf	molecular surface (Gaussian density surface)
MSMS	molecular surface as determined by the program MSMS
Surf	molecular surface as determined by SURF
VolumeSlice	display a texture mapped slice from a volumetric data set
Isosurface	display an isovalue surface from a volumetric data set
FieldLines	field lines generated by integrating particles by volume gradient vectors
Orbital	molecular orbital selected by wavefunction type, spin, excitation, and orbital ID
Beads	per-residue approximate bounding spheres
Dotted	dotted van der Waals spheres for atoms, no bonds
Solvent	dotted representation of the solvent accessible surface