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Pappulab/metastable-condensates
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All use this python enviroment -conda activate thtfit_env --------------------------------------------------------------------------------------------------------------- Fitting ThT Data -Folder: ThT_Fitting_Each_Condition_500_max_test_files -Run: python Revised_Model_Optimizer_{construct}_{concentration}_Day_{day}.py -Each file need to change the concentration and reference to construct, concentration, and day -Also make sure using right csat and optimize for a given time cutoff given curve -Generally uses best guess from previous concentration for initial conditions - best_guess_{construct}_{prevconcentration}_Day_{day}.txt -If that doesn't lead to a fit a file called initial_guess_{construct}_{currconcentration}_Day_{day}.txt is used which was sometimes just modulated as need to reduce the residuals Monomer Fraction in Each Phase -Folder: Plot_Protein_Fraction -Run: python Revised_Model_Runner_Read_In_Best_Params.py -Step size and steps listed in Settings_Revised_Eq.py and were step_size = 0.001, num_steps = 500000, equil_steps = 0 -However since using equation to split dilute and dense based on rates equilibriation is not necessary -Outputs total protein concentration in each phase as a function of the step Plot titration of kdilden and kdendil -Folder: Paramter_Titration -Run: python Revised_Model_Runner_200_mix.py -Data generated in Data_kdil_kden_titration -Plotted using plot_kdilden_kdendil_titration.ipynb
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