How to colour the whole segment, a single residue or a residue type or a single atom or all atoms of one type with a specific colours

1. Go to View - Atom colour.
2. To colour...
   1. a whole segment with one colour, type in the "Segment"-box the number of the segment.
      OR
      Leave * in the boxes and select only the molecule you want to colour from the "Molecule list"-box in the "GUI"-window.
   2. a single residue, type the residue number in the "Residue"-box.
   3. e.g. all aspartic acids with a specific colour, type "ASP*" in the "Residue"-box.
   4. a single atom, type the atom number in the "Atom"-box.
   5. e.g. all carbons with one colour, type "C*" in the "Atom"-box.
3. Choose colour by clicking the Choose colour-button, pick a colour and click OK
4. Click Apply.

• To reset the original atom colours, click Reset atom colour-button.
• If there is charge information available, you can colour the surface according to the charge. Just click the checkbox in "Colour by charge" and determine the minimum and maximum values for the charges.
• To check the atom and residue numbering, go to View - Atom tree. An "Atom tree"-window pops up, where the atoms of a molecule or amino acid sequence of a protein is listed.

How to colour protein secondary structure elements with specific colours

1. Mark "Append to stack"
2. Type "CA" to the "Atoms"-box.
3. Click on the button Click for information
4. Choose a Plumber type (Tube, Ribbon, Solid helix, Flat helix, Arrow or Strand)
5. Choose colour by clicking the Color-button, pick a colour and click OK.
6. Mark either one HELIX or one SHEET in the "Secondary Structure"-window.
7. Click Create all plumbers of this kind.
8. Now you should see either the helices or the strands depending on what you chose.
9. Do steps 4-9 for the secondary structure element you did not colour at the previous time and the loops regions.