It is possible to color molecules in MarvinView by certain properties of their atoms. These properties are stored in an additional data field in an SDfile as a property list. The name of the data field can be specified for MarvinView by the
-t parameter. The property list contains one or more property symbols for each atom, by the order of the atoms. The properties of different atoms are separated by a semicolon. The number of specified atoms must match the number of atoms in the molecule. If an atom has two or more properties, they are separated by a slash.
the first two atoms have no properties.
the third atom has property denoted by symbol "a"
the fourth atom has both property b and c
The color profile for each data field labels is stored in a configuration file in "symbol = value" format. The file name of the color profile is an input parameter of MarvinView (-p).
a = red b = blue c = green d = black e = navy f = maroon a/d = purple b/d = lime a/c = aqua empty = #808080 other = fuchsia
All property symbols and their combinations (separated by slash character) can have own colors assigned. There are two special symbols: "empty" and "other". Atoms not having any property will be displayed with the color of "empty". The rest of atoms are displayed with the color of "other" (undefined combinations). MarvinView supports the 16 color names of the HTML standard (see below), but it is allowed to assign any valid RGB color value to symbols.