text: user6610: I'm a beginner to structural biology and for fun, calculated the tortional angles of some 100, 000 proteins. Here is my Ramachandran plot:  
  When I went to look for "canonical" Ramachandran plots, I discovered most researchers overlay a "contour" plot of allowed torsional angles (see below). My two questions are:
  
  How are the distributions (ie. countours) of protein secondary structures calculated/derived? (ie. How do I "cluster" these into beta-sheets, alpha helices?)
  How can I derive them myself?
  
  
  
  user4622: To expand on Matteo Ferla's comment as an answer, there are two approaches to getting these "allowed" contours:
  
  From probabilities found in observed crystal structures. You could imagine plotting a Ramachandran plot for the whole PDB and colouring the points by assigned secondary structure from DSSP. The contours would then be regions that encompass e.g. 99% of alpha-helical residues, or 99% of all residues. In doing this you would notice for example that glycine can adopt more regions of the Ramachandran space that other amino acids. PROCHECK is software that scores a protein based partly on the likelihood of the phi/psi angles of each residue.
  From reasoning about the chemistry of the secondary structure of proteins. Only certain phi/psi combinations allow the i -> i + 4 pattern in an alpha-helix or the alternating up/down sidechain pattern in a beta-strand.
  
  
original_text: 6610: <p>I'm a beginner to structural biology and for fun, calculated the tortional angles of some 100, 000 proteins. Here is my Ramachandran plot:  <a href="https://i.stack.imgur.com/UxBRk.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/UxBRk.png" alt="enter image description here"></a></p>
  
  <p>When I went to look for "canonical" Ramachandran plots, I discovered most researchers overlay a "contour" plot of allowed torsional angles (see below). My two questions are:</p>
  
  <ul>
  <li>How are the distributions (ie. <strong>countours</strong>) of protein secondary structures calculated/derived? (ie. How do I "cluster" these into beta-sheets, alpha helices?)</li>
  <li>How can I derive them myself?</li>
  </ul>
  
  <p><a href="https://i.stack.imgur.com/uWdUk.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/uWdUk.jpg" alt="enter image description here"></a></p>
   4622: <p>To expand on Matteo Ferla's comment as an answer, there are two approaches to getting these "allowed" contours:</p>
  
  <ol>
  <li><p>From probabilities found in observed crystal structures. You could imagine plotting a Ramachandran plot for the whole PDB and colouring the points by assigned secondary structure from <a href="https://swift.cmbi.umcn.nl/gv/dssp" rel="nofollow noreferrer">DSSP</a>. The contours would then be regions that encompass e.g. 99% of alpha-helical residues, or 99% of all residues. In doing this you would notice for example that glycine can adopt more regions of the Ramachandran space that other amino acids. <a href="https://www.ebi.ac.uk/thornton-srv/software/PROCHECK" rel="nofollow noreferrer">PROCHECK</a> is software that scores a protein based partly on the likelihood of the phi/psi angles of each residue.</p></li>
  <li><p>From reasoning about the chemistry of the secondary structure of proteins. Only certain phi/psi combinations allow the i -> i + 4 pattern in an alpha-helix or the alternating up/down sidechain pattern in a beta-strand.</p></li>
  </ol>
  