A Swiss Army Knife for MM Analysis
esra is a lean and mean library of portable, flexible, generic, ![[WWW]](/rightsidebar/img/moin-www.png){kind=small}
scriptable, buzzword-compatible and reasonably high-performance routines for the analysis of molecular mechanics data ( GROMOS96 molecular dynamics trajectories, mostly).
It is meant to expose routines for file parsing/generation and statistical/structural analyses (secondary structure assignment, hydrogen bonding, 3D-densities, RMSD's, NOE distance violations etc.), to be used by higher-level interactive interfaces, such as mathematica, matlab and jython (for shell utilities).
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Creating a 2D-Plot of an RMSD matrix is just a few lines of mathematica-code. |
Support for PDB and XPLOR-formatted output allows for easy visualization (including the creation of movies and 3D-density plots) via e.g. pyMol.
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3D-densities of water atoms around a monosaccharide. The trajectory fitting and density calculation were performed in esra, dumped to an XPLOR file and visualized in pyMol. |
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Quick Links
ScriptRepository (overview of supported frontends and examples)
Please post your comments, suggestions and complaints on the mailing list, or create an account on the wiki and start editing.
News
July 4th 2006: esra 0.8 available
We are pleased to announce version 0.8.0, which introduces lots of bugfixes, extra unit tests, documentation and all the remaining functionality needed to perform simple molecular dynamics and Monte-Carlo simulations. Check out md.py in the pyEsra script collection!
April 7th 2006: esra 0.5 available
Code cleanup and a bunch of features, including bundles of Jython scripts and Mathematica notebooks. One step from the raw data to the finished and annotated plot.
Nov 19th 2005: esra 0.3 available
basic force field support should make the second stable release of esra a useful tool for docking studies. stay tuned.
Sep 28th 2005: esra 0.1 available
This is the first stable release. It features the basic building blocks for the analysis of molecular mechanics data. Its IO routines support formats that include GROMOS96, PDB, vmd/AMBER, and SYBYL/mol2. It has a Java linear algebra library, basic (geometric) analysis tools such as rmsds, fitting procedures, distance/angle/dihedral measurements, and hydrogen bond analysis. For thanks, see the CreditsList.