VMD User's Guide

There are 1041 colors available in VMD, with color ids ranging from 0 to 1040. The first 17 are,in order: blue, red, gray, orange, yellow, tan, silver, green, white, pink, cyan, purple, lime, mauve,ochre, iceblue, and black.The next group of 1024 colors (from 17 to 1040) are colors used in the color map, These can beset to one of several ranges with the Color form or the color text command: red→green→blue,red→white→blue, or black→white, etc. There are no names for the specific colors. The color mapwill be discussed in more detail in a section to follow.5.2.1 Color categoriesVMD maintains a database of the colors used for the molecules and the other graphical objects inthe display window. The database consists of several color categories; each color category containsa list of names, and each name is assigned a color. For example, there is a Resname color category,and within this category there are many names; one for each of the available residue names. Someof these are ALA, CYS, andPRO. Each name can be assigned a color from a list of 17 available colorscalled the color map. The RGB value of each color can be modified directly in the Color form[§4.4.9]. To color items in a gradation manner, there are additional 1024 colors used in the colorscale [§5.2.4].The different color categories in VMD are listed in table 5.2. The Color form can be used tochange the assignment of colors to the names in each of these categories. For example, to changethe color used to draw Arginine residues when molecules are colored by residue, you would use theColor form, select the ‘Resname’ category, select the ‘Arg’ name there, and then pick the color touse for Arginine’s from the list of colors next to the names.CategoryDisplayAxesStageNameTypeResnameChainSegnameMoleculeHighlightRestypeStructureSurfaceLabelsContentsThe background colorThe components of the axesThe colors for the checkboard stageThe available atom names (color by Name)The available atom types (color by Type)The residue names (color by ResName)The one-character chain identifier.The segment names (color by SegName)The names assigned to each molecule (color by Molecule)The protein, nucleic, and non-backbone colorsThe residue types (color by ResType)The secondary structure type (helix, sheet, coil) (color by Structure)The surface typesThe different labels (atoms, bonds, etc.)Table 5.2: Color categories used in VMD.5.2.2 Coloring MethodsAs described in chapter 5, each representation for a molecule has a specific coloring method. Thecoloring method determines how the color for each atom in the representation (view) is determined.These different methods use the colors assigned to the names in the categories listed above, and use66