The outputted results from GAJOE in EOM

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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Maniac_from_CPH
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The outputted results from GAJOE in EOM

#1 Post by Maniac_from_CPH » 2019.06.04 15:01

Hello everyone,

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.

kind regards,
Martin

mawhite
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Location: UTMB, Galveston, TX

Re: The outputted results from GAJOE in EOM

#2 Post by mawhite » 2019.11.05 19:58

Martin,

Based on my understanding of the EOM/Gajoe programs the distributions and the output PDB are not directly related. Gajoe by default runs 100 evolutionary MC optimizations to produce a unique best-fit ensemble of from 1-6 pdbs. The Rg of the selected PBS from all 100 runs seems to be used to produce the distributions. The best-fitting ensemble of these 100 is the one that is output at the end in the pdbs/ folder.

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