The reproducibility of the calculation is examined by running the same calculation a number of times (in this case, 5 times). The script get_j.pl is used to extract the value of the Jfactor and the associated error from the "analyze_chains.header" files contained in the subdirectories. Notice that the error associated with each J-factor underestimates the actual variance of the final calculated J-factors. This is due to the use of "half-chains" in the generation of "whole-chains". The "Independent Calculations" parameter helps to minimize this effect, see the section (blah) for further details.

The reproducibilty of the calculation would be better by increasing the number of whole chains analyzed (as shown below) and/or increasing the number of independent calculations.

# whole chains=10^9 (icalcs=100) 
bass (lapham): [~/cyclize/samples/atract]> get_j.pl atract_example_*/an*header
directory name                  J factor     Error
atract_example_1                   53.45    (2.15)
atract_example_2                   58.96    (2.15)
atract_example_3                   56.19    (2.14)
atract_example_4                   56.14    (2.11)
atract_example_5                   71.11    (2.65)
atract_example_6                   69.98    (2.58)
atract_example_7                   68.31    (2.41)
atract_example_8                   64.25    (2.40)
atract_example_9                   65.12    (2.51)
atract_example_10                  63.58    (2.38)
Repeating this experiment with a larger number of chains:

# whole chains=10^10 (icalcs=100) 

bass (lapham): [~/cyclize/samples/atract]> get_j.pl atract_example_*/an*header
directory name                  J factor     Error
atract_example_1                   61.69    (2.19)
atract_example_2                   71.55    (2.49)
atract_example_3                   67.84    (2.36)
atract_example_4                   63.20    (2.29)
atract_example_5                   68.14    (2.37)
atract_example_6                   64.07    (2.30)
atract_example_7                   68.63    (2.53)
atract_example_8                   74.83    (2.72)
atract_example_9                   67.34    (2.40)
atract_example_10                  70.57    (2.37)


Graphically...