Metadata-Version: 1.1
Name: RotamerConvolveMD
Version: 1.2.0
Summary: Analysis of spin label distances over structural ensembles
Home-page: https://github.com/MDAnalysis/RotamerConvolveMD
Author: Philip W. Fowler
Author-email: philip.fowler@ndm.ox.ac.uk
License: GPL 2
Description: .. -*- mode: rst; coding: utf-8 -*-
        
        ======================================
         MTSL Rotamer fitting to trajectories
        ======================================
        
        :Author:    Philip W Fowler, Oliver Beckstein
        :Year:      2013
        :Licence:   GNU Public Licence, version 2 (or higher)
        :Copyright: © 2013 Philip W Fowler, Oliver Beckstein
        :Citation:  LS Stelzl, PW Fowler, MSP Sansom, O Beckstein. J Mol Biol
                    426 (2014), 735-751. doi: 10.1016/j.jmb.2013.10.024
                    
        This package contains the *MTSL rotamer library R1A_298K* provided by
        `Gunnar Jeschke`_, which is also published under the GPL with his
        permission.
        
        Summary
        =======
        
        This package analyses molecular dynamics trajectories or
        conformational ensembles in terms of spin-label distances as probed in
        double electron-electron resonance (DEER) experiments. The spin labels
        are fitted on trajectories and the spin label mobility is taken into
        account using a rotamer library.
        
        
        Background
        ==========
        
        Double electron electron spin resonance (DEER) is an EPR technique for
        measuring distances between two spin labels that have been covalently
        attached to a protein. Two cysteine residues are introduced into the
        protein and subsequently labelled. The positions are chosen to report
        on the expected conformational change. A commonly used spin label is
        (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl)-methanethiosulfonate
        (MTSL). MTSL has a linker with five rotatable bonds and is therefore
        very flexible. The distance distributions between the two spin labels
        measured by experiments are typically broad and often multi-modal. The
        distributions are therefore a convolution of the flexibility of the
        MTSL spin label and the conformational spread of the proteins in the
        sample. To ensure that we compared like with like we developed a
        method that 
        
        1. maps rotamer libraries of the MTSL spin label onto each position,
        
        2. discards those rotamers that sterically clash with the protein
           (typically distances <2 Å) and
        
        3. calculates all (weighted) distance pairs between the remaining
           rotamers and 
        
        4. thereby estimates a distance distribution for that structure. 
        
        The code was written in Python using the MDAnalysis_ library
        [Michaud-Agrawal2011]_ and a published rotamer library for MTSL
        [Polyhach2011]_. It is available for download from the MDAnalysis
        website, https://github.com/MDAnalysis/RotamerConvolveMD .
        
        Our approach improves upon the existing method [Polyhach2011]_ by
        increasing computational efficiency and implementing, via the
        MDAnalysis library, analysis of ensembles of hundreds of structures,
        which allowed us to estimate distance distributions for entire
        simulation trajectories. 
        
        Examples of the application of this approach can be found in
        [Stelzl2014]_.
        
        
        Installation
        ============
        
        Typically, install the package with ::
        
           python setup.py install --user
        
        (see also the file ``INSTALL.rst``)
        
        This will automatically install MDAnalysis and other dependencies. If
        problems arise, try installing MDAnalysis first (see
        http://www.mdanalysis.org for help).
        
        Analysis is performed with the script ``convolve-mtss-rotamers.py``,
        which will have been installed in your ``bin`` directory. You might
        have to add the bin directory to your ``PATH``. Consult your Python
        documentation for the details although often this will be
        ``~/.local/bin`` (for a ``--user`` installation or ``/usr/local/bin``
        for site-wide installation). 
        
        
        Usage
        =====
        
        Analysis is performed with the script
        ``convolve-mtss-rotamers.py``. It takes as input
        
        * a topology or structure file (PSF, GRO, PDB, ... any `topology
          format`_ recognized by MDAnalysis)
        * a trajectory (DCD, XTC, TRR, ... any `trajectory format`_ that
          MDAnalysis can read)
        
        A typical invocation::
        
           convolve-mtss-rotamers.py --resid 47 330  --histogramBins 0 80 1  --clashDistance 2.2  \
                  --output "dat/peptso-xrd"  --dcdfilename "dcd/peptso-xrd-47-330" \
                  peptso.gro peptso.xtc 
        
        It loads the MD trajectory from the topology ``peptso.gro`` and the
        trajectory ``peptso.xtc``. The ``--resid`` pair is required and
        denotes the residue numbers (in the topology) to which the MTSSL spin
        labels would be attached. Rotamers that overlap with protein atoms as
        measured by an atom-atom distance smaller than the ``--clashDistance``
        will be discarded and not counted in the distance calculations. For
        further explanations see the ``--help`` option.
        
        For an example, see ``doc/example`` in the source distribution. The
        example can also be run to test the installation as reference output
        is provided.
          
        
        Help
        ====
        
        If you have questions or problems installing the package then ask on
        the MDAnalysis user mailing list:
        http://groups.google.com/group/mdnalysis-discussion
        
        	
        References
        ==========
        
        .. Links
        .. -----
        
        .. _MDAnalysis: http://www.mdanalysis.org
        .. _Gunnar Jeschke: http://www.epr.ethz.ch/
        .. _topology format: 
           https://pythonhosted.org/MDAnalysis/documentation_pages/topology/init.html#supported-topology-formats
        .. _trajectory format:
           https://pythonhosted.org/MDAnalysis/documentation_pages/coordinates/init.html#id1
        
        .. Articles
        .. --------
        
        .. [Michaud-Agrawal2011] N. Michaud-Agrawal, E. J. Denning,
           T. B. Woolf, and O. Beckstein. MDAnalysis: A toolkit for the
           analysis of molecular dynamics simulations. J Comp Chem,
           32:2319-2327, 2011. doi:`10.1002/jcc.21787`_. http://www.mdanalysis.org
        
        .. _`10.1002/jcc.21787`: http://doi.org/10.1002/jcc.21787
        
        .. [Polyhach2011] Y. Polyhach, E. Bordignon, and G. Jeschke. Rotamer
           libraries of spin labelled cysteines for protein
           studies. Phys. Chem. Chem. Phys., 13:2356-2366, 2011. 
           doi: `10.1039/C0CP01865A`_.
        
        .. _`10.1039/C0CP01865A`: http://dx.doi.org/10.1039/C0CP01865A
        
        .. [Stelzl2014] L. S. Stelz, P. W. Fowler, M. S. P. Sansom, and
           O. Beckstein. Flexible gates generate occluded intermediates in the
           transport cycle of LacY. J Mol Biol, 426:735-751, 2013. 
           doi: `10.1016/j.jmb.2013.10.024`_ 
        
        .. _`10.1016/j.jmb.2013.10.024`: http://dx.doi.org/10.1016/j.jmb.2013.10.024
        
        
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires: numpy (>=1.6)
Requires: MDAnalysis (>=0.11.0)
Provides: rotcon
