When running GAJOE one is asked for how many times the GA should be repeated, with the default being 100 times. In the manual it says:
"Number of times (cycles) to repeat the genetic algorithm. It is recommended to run the genetic algorithm at least 50 times. Please note that final distributions are based on the repetition of the genetic algorithm. Selecting a small number of repetitions may generate nonsensical final distributions"
Can someone explain in more detail how the final distribution is produced from the repetitions? I would just like to know if it is the best fit from each repetition which is pooled together to create the final distributions, or if there is some other approach.
My reason for asking is that the logfile from GAJOE lists 12 pdbs as the ensemble fit, which is nowhere near enough structures to generate the somewhat smooth distributions that are found in the outputs (e.g. in Rg_distr_001_1.txt). The final distributions are of course not as smooth as the starting pool, but from 12 structures/Rgs/Dmax etc. you would have a very jagged distribution.
Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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