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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




Subsections
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Next: Lines Up: Molecular Drawing Methods Previous: Molecular Drawing Methods   Contents   Index
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