The SIBYLS Beamline: MES (Minimal Ensemble Search)

MES (Minimal Ensemble Search)

Considering the flexibility of domains, the coexistence of different conformations that

contribute to the experimental scattering curve has to be taken into account. Based on the ensemble optimization method described by Bernado et al. (Bernado et al, 2007) we have developed an algorithm which searches for the minimal ensemble (Minimal Ensemble Search (MES)) of the conformations from the pool of all generated conformations. The multiconformational scattering I(q) from such a minimal ensemble is computed by averaging the individual scattering patterns from the conformers (Pelikan et al. 2009)

Written by: Martin Pelikan & Michal Hammel

Reference: Pelikan, M., Hura, G.L., and Hammel, M. (2009). Structure and Flexibility within proteins as identified through small angle X-ray scattering. General Physiology and Biophysics 28, 174-189

download : Pelikan2009.pdf

download program : MES

Hardware platforms: LINUX 32bit free available for academic use

USAGE on bl1231.als.lbl.gov

> ssh username@bl1231.als.lbl.gov # ask MH for access

> ssh crush !!!!!!!!

> cd to your directory with your scattering profiles

1. First you will need to clean head lines in the fit_files produced by FOXS. And have only one empty line at the top. please see the example for the *fit file. You may used FOXS web app to calculate fit_files.

2. Make filelist of the fit_files with the experimental_dat file at the top of the filelist ( experimental data containing q, I(q), SD example for experimental_dat )

3. Usage: mes filelist

sibyls@crush:eap/test 75% mes list

Output:
Selected conformers and + weighting in %/100 will be printed at the end of the run.
avg_optimal is the MES -fit file with chi2 listed in the first line

for more details about mes usage see README