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 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.To run MES program you will need to cut head lines in the *fit files produced by CRYSOL. please see the *fit file how many lines are garbage.

example file.fit (#lines garbage)

sibyls@crush:eap/test 75% cut_the_data.pl 5 *fit ◄┘

Usage: cut_the_data.pl #number (1-9 number of lines to cut) *fit (all *fit files)

2.To run MES you need list of the files starting with *dat file ( experimental data containing q, I(q), SD example for *dat ) followed by *fit files (example for list )

sibyls@crush:eap/test 75% mes list --subset-size 5 > mes.out & ◄┘

Usage: mes list (file list) --subset-size 5 ( subset size 1,2,3,4,5 ... default 20 )

Output:
mes.out       at the end of the files are listed selected conformers and + weighting in %/100
avg_optimal    MES -fit file with chi2 listed in the first line

for more details about   mes usage see README