Is this what you mean?

^(ATOM|HETATM).*GLN

This will match any line which starts with either 'ATOM' or 'HETATM', followed by any string of arbitrary characters, followed by the string 'GLN'.

This indeed works but I do think I need to be a bit more specific. Lets look again at the line:

ATOM 14 CA GLN A 2 -27.648 -9.581 30.325 1.00 10.00

My goal is to have both the 'ATOM' string and the 'GLN' string colored differently.

Using ^(ATOM|HETATM)\b I can color the ATOM part. Using \bGLN\b I can color the GLN part.

The problem is that I only want the GLN part to be colored if the line starts with ATOM. In your reply the complete part starting with ATOM up to GLN gets colored.

Marc