VMD User's Guide

5.1.19 BeadsA bounding sphere is drawn in place of each residue in the atom selection. This representation canbe used as a crude means of drawing very large structures in a space filling representation and canbe particularly useful for animating trajectories.5.1.20 DottedSame as ‘VDW’ [§ 5.1.6] except that the spheres are drawn dotted instead of solid. That is, a dot isplaced at each of the vertices of the triangle making up each sphere. This can be used, for instance,to imitate a surface representation.5.1.21 SolventThis method is similar in spirit to the ‘Dotted’ [§ 5.1.20] representation in that it gives a quickestimate of the molecular surface with a collection of dots. However, it goes above and beyond theDotted option by giving a more uniform coverage of the surface. The method that VMD uses tocheck for overlaps isn’t technically correct, but it is fast and works quite well. A technical descriptionof the algorithm is as follows:For each point of the surface distribution (of radius r = atom radius + probe radius) of atomi, check each of the atoms j to which it is covalently bound. If the point is too close to j, don’tdisplay it. Also, if the point is too close to any neighbor k of j (k ≠ i) then don’t draw it. Thisis fast since there aren’t that many neighbors to check, but it doesn’t omit parts of the surface incontact with atoms which aren’t one or two bonds away. This can be considered a good thing sinceyou might get a better idea of the contact surface.There are three parameters for this option. One is the Probe Radius, which was mentionedin the description. If the probe radius is too large, the problem of over-lapping surfaces betweennon-connected atoms becomes more apparent. The second is Detail Level, which should probably berenamed ”Density” as it determines the surface density of the distributions. The higher the detail,the higher the density. The final option is the Representation Method. By default the surface isdrawn as a collection of points, but a point is a pixel in size regardless of the scale of the molecule,so when scaled small the surface density appears high, and when scaled large, the density appearslow. Method 2 draws little plus signs instead of points, which does scale better so the densityappears more contant. Method 3 draw lines between the surface points that are on the same atom,but makes no attempt to connect the two spheres.Thanks to Jan Hermans for implementation pointers and thanks again to Jon Leech for the codeto compute the uniform point distributions. That code was included as part of the 1.x distribution.5.2 Coloring MethodsVMD maintains a database of the colors used for the molecules and other graphical objects whichare visible in the display window. It keeps track of• color name definitions - its RGB value;• mappings from a color category to color name - so residue name MET is colored yellow• the current color scale - red to white to blue, and several related parameters65