Figure 2

Example code. At the top (Code I), a detailed example for the computation of the B-factors using the provided low-level routines is shown. At the bottom (Code II), the function call of simc is shown with all parameters given to the function to compute the values of Figure 4. The parameter alpha represents the strength of peptide bonds and is set to 82 per default, the parameter cuts denoting the squared cutoff distance for a contact has a default value of 169. If no interaction weighting matrix is given, the MJ and KE matrices [22, 23] are used to describe the specific intra- and interchain interaction strengths, respectively, eventually averaged if mj.avg = TRUE. If the parameter bfacs is set TRUE, for each broken contact the computed B-factors are written into files. Frobenius norms are only computed and returned if frob = TRUE. With the parameter cluster it is possible to provide an initialized cluster for a parallel computation.