For a given segment of polypeptide chain ("loop") this method scans the PDB database for segments that have similar conformations (within "vicinity") and calculates relative frequencies of residues at each position. Thus you can find out if certain residues might be preferred in some positions, for instance in beta-turns depending on the type a glycine or a proline might be preferred.

• Read in a protein structure and convert to an ICM object.
• Select the residues in the loop.
• MolMechanics/Loop/Preferred residues
• Enter a vicinity value (see: http://www.molsoft.com/man/reals.html#vicinity).
• Click OK.
• A table of the relative frequencies of residues at each position are reported.