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choderalab / AURKA_UMN

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GLN185 is present in every trajectory, even when mutation should be present #25

Closed juliebehr closed 8 years ago

juliebehr commented 8 years ago

https://github.com/choderalab/AURKA_UMN/tree/fah-pdbs/fah-pdbs

juliebehr commented 8 years ago

Calculating the hydrogen bonds acting only on the sidechain of Q185, instead of the entire residue, eliminated differences between runs -- WT vs "Q185L"

jchodera commented 8 years ago

Was this an issue in the initial system setup or in the analysis end of things?

juliebehr commented 8 years ago

Found input pdbs -- no mutants

jchodera commented 8 years ago

Ah, OK. We can always set up more runs.

juliebehr commented 8 years ago

I'm not sure how, then, to account for the apparent differences between the runs? Can I aggregate all the data for both projects and treat it as 250 clones of 1OL5 and 1OL7 WT?

jchodera commented 8 years ago

Well, I guess this explains why there isn't significant difference in the averages: https://github.com/choderalab/AURKA_UMN/blob/fah-pdbs/plots/AURKA-hydrogen-bonds-11410-all-runs.png https://github.com/choderalab/AURKA_UMN/blob/fah-pdbs/plots/AURKA-hydrogen-bonds-11411-all-runs.png

jchodera commented 8 years ago

I think you can go ahead and aggregate the data for both projects as you suggest.

I'd convert these plots into probability densities instead of numbers of trajectories.

juliebehr commented 8 years ago

Slight refactoring of the setup script and updating to pdbfixer-dev seems to have fixed this problem! Currently generating the new serialized XMLs on src -- first with the crystallographic waters still saved, next will remove them.

juliebehr commented 8 years ago

FaH projects 11412-11417