1. You need to explicitly write out the Matlab commands you used to extract and plot the CA coordinates and the contact matrix. That does not mean you needed to include the functions pickCA() and make_contmap. Rather, you should just show your calls to these functions. As a rule of thumb, any code that you write by yourself or significantly modify from what is given in class should be included in your reports. Any code provided in class that you use "as is" need not be included.
2. You needed to use the contact matrix for secondary structure analysis.
A partial goal of this exercise was to show that the contact matrix is a useful
tool for deteremining secondary structure.
(Note: On some homeworks, this comment may have been swapped with comment #3)
3. You did not include any structural analysis, or your analysis has been
too cursory. For instance, identifying only one or two elements of secondary
structure on the 3D-coordinate plot is insufficient.
(Note: On some homeworks, this comment may have been swapped with comment #2)
4. You did not use the right formula for computing the distance between two matrices. According to the definition given in the homework, dist(A,B) = norm(A-B). The Matlab function norm() computes the norm of a matrix, and it should have been used to find the distance between CA and N coordinate matrices.
5. You did not provide the code for computing the geometric center of a protein. While the script was given in the class notes, it was not provided in function form. If you wrote a function that re-centers a coordinate matrix, then you needed to include that function in your report.