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 and/or increasing the number of independent calculations.

$icalcs=100; $whole chains=10^9

bass (lapham): [~/cyclize/samples/flex]> get_j.pl flex_example_*/an*header
directory name                  J factor     Error
flex_example_1                   2346.50   (54.93)
flex_example_2                   2326.38   (54.29)
flex_example_3                   2355.60   (55.04)
flex_example_4                   2293.20   (53.75)
flex_example_5                   2288.61   (53.26)
flex_example_6                   2405.08   (56.65)
flex_example_7                   2334.36   (55.55)
flex_example_8                   2340.18   (54.45)
flex_example_9                   2309.38   (54.48)
flex_example_10                  2366.29   (55.48)

Repeating this experiment with a larger number of chains:

$icalcs=100; $whole chains=10^10

corona (lapham): [~/cyclize/samples/flex2]> cat flex2.out 
directory name                  J factor     Error
flex_example_1                   2418.14   (67.20)
flex_example_2                   2247.38   (61.35)
flex_example_3                   2387.73   (65.37)
flex_example_4                   2390.99   (65.26)
flex_example_5                   2254.16   (62.00)
flex_example_6                   2293.28   (61.72)
flex_example_7                   2332.82   (64.24)
flex_example_8                   2405.18   (65.37)
flex_example_9                   2232.27   (61.08)
flex_example_10                  2347.26   (64.19)