The tutorial is for Hemoglobin.  We will discuss hemoglobin in class and students are not allowed to use it for the protein structure project.  The images presented are designed to assist students in generating their own images.

1.  The Hemoglobin file for this tutorial is 1A3N which shows the protein in the deoxygenated state.  Use the designation for your protein to search the Protein Data Bank and download the coordinates as described on the protein project page.  When you open the file in RasMol it will look like this:

2.  Type the command "set background white" to change the background (Please note that neither of these images would be suitable for submission with your paper):

3.  To color the four polypeptide chains of the hemoglobin protein use the "Chain" option under the Colours menu in RasMol.  Then type in "select hem" and hit return.  Color the heme red by typing "color red" and then use "Ball & Stick" command from the Display menu.  This could provide an introductory image for your paper.  In the paper one could discuss the 4 polypeptide chains and the significance of the heme prosthetic group.  Typing in a "select ligand" command would also select the heme group for this protein and should select ligands or nucleotides associated with student proteins.

4.  To show secondary structure present in a protein, type "select protein" as the last command selected the heme groups.  Then use the "Ribbons" command from the Display menu.  To color the secondary structure, use the "Structure" command from the Colours menu.  This image shows that hemoglobin is mostly alpha-helical in structure and contains no beta-sheets.  I would suggest not using this as an image for your paper, but there are proteins with interesting secondary structural elements that would be useful for students' papers.  The heme groups are colored blue in this image so they stand out against the red alpha helices.

Page 2: The next page of the tutorial discusses how to highlight specific residues and atoms