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)


Version 1.x  Copyright © Michal 2008

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


> ssh     # 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   

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