Bayesian Ensemble Estimation from SAS (BEES)


Accessibility

The BEES module is available from the "Bayesian Ensemble Estimator" selection in the Analyze section of the main menu.


Basic Usage

The BEES module is designed to help users fit their SAS data with an ensemble model built from a library of candidate states. Populations of states in different combinations of candidate profiles are reweighted using a Bayesian Monte Carlo (BMC) approach, and the module will select the best model that balances both a high quality goodness-of-fit and a minimum number of contributing states.


Notes


Standard BEES Usage


Inputs


BasicInputs


In order to recreate the inputs used above, users should download the following files:


Outputs


BasicOutputs


Once the best ensemble of candidate states is determined, BEES will print information regarding the model (shown above), namely: the contributing scattering states and their populations, observed error in population, and individual ability to fit experimental data, as well as the goodness-of-fit metrics for the ensemble model and its associated AIC or BIC value. Also at the conclusion of the run, BEES will generate interactive plots below the progress bar that contain the best ensemble's fit to the experimental SAS profile, along with the model residual errors in the fit.

As noted in the output, results are also stored in the form of several files that are saved to the ./[runname]/bayesianensembleestimator/ subdirectory:

./run_0/bayesian_ensemble_estimator/run_0_all_models.dat
./run_0/bayesian_ensemble_estimator/run_0_ensemble_sas.int
./run_0/bayesian_ensemble_estimator/run_0_final_model.dat
./run_0/bayesian_ensemble_estimator/run_0_plots.html

The separate panels of the *_plots.html contain different levels of information regarding the BEES-observed models:


Using BEES with Auxiliary Data


Advanced BEES Inputs


AuxiliaryInputs


Users that wish to recreate the inputs shown above should download the following files:


Outputs with Auxiliary Spectra


AuxiliaryOutputs


Most Advanced Options in BEES will not alter the outputs of the program, with the exception being the case in which auxiliary data was supplied. If an auxiliary data set is supplied, then the SASSIE-web will now create an additional set of plots beneath the scattering profile figures that present the ensemble fit to the auxiliary spectrum and the associated error in the fit. As noted previously, results are also stored in the form of several files that are saved to the ./[runname]/bayesian_ensemble_estimator/ subdirectory:

./run_0/bayesian_ensemble_estimator/run_0_all_models.dat
./run_0/bayesian_ensemble_estimator/run_0_ensemble_aux.dat*
./run_0/bayesian_ensemble_estimator/run_0_ensemble_sas.int
./run_0/bayesian_ensemble_estimator/run_0_final_model.dat
./run_0/bayesian_ensemble_estimator/run_0_plots.html

"*" denotes the additional file that is only produced if an auxiliary data file is supplied. This file is a 1-column text file that contains the values for the ensemble model at each auxiliary measurement. An example of this output can be found here.

Furthermore, the first and second tabs of the HTML page will also possess spectra for the auxiliary data alongside the SAS profiles. An example be found here.


Limitations


References and Citations

  1. BEES: Bayesian Ensemble Estimation from SAS, a SASSIE-web Module. S. Bowerman, J.E. Curtis, J. Clayton, E.H. Brookes, and J. Wereszczysnki. In Preparation.
  2. Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations. S. Bowerman, A.S.J.B. Rana, A. Rice, G.H. Pham, E.R. Strieter, and J. Wereszczynski. J. Chem. Theory Comput., 13, 2418 (2017). BIBTEX EndNote Plain Text