VMD User's Guide

Representation stylesLinesBondsDynamicBondsHBondsPointsVDWCPKLicoriceTraceTubeRibbonsNewRibbonsCartoonNewCartoonMSMSSurfBeadsVolumeSliceIsosurfaceDottedSolventDescriptionsimple lines for bonds, points for atomslighted cylinders for bondsdynamically calculated distance-based bondsdisplay hydrogen bondsjust points for atoms, no bondssolid van der Waal spheres for atoms, no bondsscaled VDW spheres, with cylinders for bondsspheres for atoms, cylinders for bonds, same radiusconnected cylindrical segments through C α atomssmooth cylindrical tube through the C α atomsflat ribbon through the C α atomssmooth ribbon through the C α atomscartoon diagram (cylinders and ribbons) based on secondary structuresmooth cartoon diagram (smooth ribbons) based on secondary structuremolecular surface as determined by the program MSMSmolecular surface as determined by SURFper-residue approximate bounding spheresdisplay a texture mapped slice from a volumetric data setdisplay an isovalue surface from a volumetric data setdotted van der Wall spheres for atoms, no bondsdotted representation of the solvent accessible surfaceTable 5.1: Molecular view representation styles.5.1.1 LinesThe default representation is ‘Lines’, which is also known as ‘wireframe’. It draws a line betweeneach atom and the atoms to which it is bonded. Both atoms have to be selected before the bondwill be drawn. The first half of each bond is colored appropriately for the first atom, while the colorof the final half corresponds to the second atom. The only parameter for the lines representationis the line Thickness.5.1.2 BondsNearly everything about this option is the same as ‘Lines’ [§ 5.1.1] except that instead of drawinga bond as a line between two atoms, a cylinder is drawn instead. To be more specific, it draws ann-sided prism, where the number of sides is determined in the Graphics form [§4.4.7] by the BondResolution control and the radius is given by the value of Bond Radius, in Angstroms. If the radiusor number of sides gets too small, the bonds are drawn as lines.In order to fine tune the bond representation, VMD does a small amount of trickery to theprisms. That is, imagine two hollow cylinders coming together so that the center of the face of onecylinder is in the same position as the center of the face of the other cylinder. Also suppose thesetwo cylinders come together at 90 degrees. Although most of these two cylinders will overlap, therewill appear to be a gap at their intersection.To correct for this problem, VMD extends both cylinders somewhat so that the far ends touch.If one looks closely, this produces more of an overlap, but it is much nicer looking than the gap.58