The colour in Jmol

Applies to:

• Atoms
• Bonds
• Cartoon and other schematic renderings
• Background
• Objects (we will not cover this)

The others inherit from the atoms, but may be defined separately.

Again:

1. select the part of the molecule you want
2. apply colour

It's not just an aesthetic issue, but a way to transmit or convey the desired information, as applies to each case. It's an important teaching tool.

Uniform colours

Schemes, or colour patterns

• a colour for each chemical element (default, CPK)
• by secondary structure
• by charge (if that information is provided in the file —not frequent)
• by position along the chain: N→C, 5'→3' (rainbow "roygb")
• a colour for each chain
• a colour for each type of amino acid or nucleotide
• by "temperature": mobility or inaccuracy
• [all described in Jmol.org website]

Demonstration.

Time for practice.

Question time: What would you like to display?