Rasmol may be downloaded from (http://www.umass.edu/microbio/rasmol/getras.htm).

Open with RASMOL the new pdb file created by HETEROalign.

File --> new

Choose the display of your preference, i.e. cartoons

Color the protein by ‘temperature’ – HETEROalign replaces the temperature factor in the pdb file with similarity scores. Red indicates the region of highest similarity between the peptides and the protein sequence while blue indicates the regions of least similarity.

Type ‘set background white’ in the command line to change the background color

type ‘select hetero and not hoh’ to display all ligands
display : spacefill
color : cpk
options : specular
to zoom hold the shift key and left click mouse and drag down
to save image use export

The region of highest similarity between RELIC's ATP affinity selected peptides and the ATP-binding protein 2MJP is shown in red.