Metadata-Version: 2.1
Name: RotamerConvolveMD
Version: 1.3.1
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
Project-URL: Documentation, https://www.mdanalysis.org/RotamerConvolveMD
Project-URL: Source, https://github.com/MDAnalysis/RotamerConvolveMD
Project-URL: Issue Tracker, https://github.com/MDAnalysis/RotamerConvolveMD/issues/
Project-URL: Mailing list, https://groups.google.com/group/mdnalysis-discussion
Description: .. -*- mode: rst; coding: utf-8 -*-
        
        ======================================
         MTSL Rotamer fitting to trajectories
        ======================================
        
        :Author:    Philip W Fowler, Oliver Beckstein, Katrin Reichel, and AUTHORS_
        :Year:      2013
        :Licence:   GNU Public Licence, version 2 (or higher)
        :Copyright: © 2013 Philip W Fowler, Oliver Beckstein,
                    © 2014–2017 AUTHORS_
        :Citation:  LS Stelzl, PW Fowler, MSP Sansom, O Beckstein. J Mol Biol
                    426 (2014), 735-751. doi: 10.1016/j.jmb.2013.10.024
        :Documentation: |docs|
        	    
        .. _AUTHORS:
           https://raw.githubusercontent.com/MDAnalysis/RotamerConvolveMD/master/AUTHORS
        
        This package contains the *MTSL rotamer library R1A_298K (2011)* and
        an *updated MTSL rotamer library R1A_298K (2015)* provided by `Gunnar
        Jeschke`_, which is also published under the GPL with his
        permission. The updated rotamer library was sent by `Gunnar Jeschke`_
        after personal discussion.
        
        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 and spin-label
        to amide protin distances as probed in paramagnetic relaxation
        enhancement (PRE) experiments. The spin labels are fitted on
        trajectories and the spin label mobility is taken into account using a
        rotamer library.
        
        For further details see the `RotamerConvolveMD documentation`_.
        
        
        
        Background
        ==========
        
        Site-directed spin labeling (SDSL) is a common technique to
        investigate structure and dynamics of macromolecular
        systems. Covalentry attached spin labels are introduced to the system
        and induce electron spin resonance.  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. Paramagnetic relaxation enhancement (PRE) is an NMR
        technique for measuring distances between a spin label and the amide
        protons of the protein backbone. One cysteine residue is introduced at
        the position of the label 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
        (DEER) or one spin label and the amide protons are 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. In the case of PRE measurements, it enables 
        the user to calculate back the transverse relaxation enhancement 
        to compare raw data without calculating the distances based on the
        experiment.
        
        In the case of MTSL, the distances are determined by considering the position of the free electron
        located between nitrogen (N1) and (O1).
        
        Examples of the application of this approach can be found in
        [Stelzl2014]_.
        
        
        Installation
        ============
        
        Typically, install the package with pip_ ::
        
           pip install RotamerConvolveMD
        
        (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`` 
        (DEER) or ``convolve-mtss-rotamers_pre.py`` (PRE), 
        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
        =====
        
        DEER
        ----
        
        Analysis for standard DEER experiments with MTSL spin labels 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" \
                --plotname "dat/peptso-xrd.pdf" \
                --outputRawDistances "dat/peptso-xrd" \
                --dcdfilename "dcd/peptso-xrd" \
                --dcdfilenameNoClashes "dcd/peptso-xrd" \
                --useNOelectron \
                --libname "MTSSL 298K 2015" \
                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. 
        The user can decide to use either N1 ``--no-useNOelectron`` or the 
        geometric midpointis N1 and O1  ``--useNOelectron``  to calculate 
        the distances. Two libraries are offered: `MTSSL 298K 2011` or 
        `MTSSL 298K 2015` (default) by defining the option ``--libname``. 
        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.
        
        
        PRE
        ---
        
        Analysis for standard PRE experiments with MTSL spin label is performed 
        with the script ``convolve-mtss-rotamers_pre.py``. Similar to the 
        analysis of DEER experiments, it takes as inputs:
        
        * 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_pre.py \
                --resid 47  \
                --clashDistance 2.2  \
                --plotname "dat/peptso-xrd-47.pdf" \
                --outputRawDistances "dat/peptso-xrd" \
                --dcdfilenameAll "dcd/peptso-xrd" \
                --dcdfilenameNoClashes "dcd/peptso-xrd" \
                --useNOelectron \
                --libname "MTSSL 298K 2015" \
                peptso.gro peptso.xtc 
        
        The ``--resid`` is required and denotes the residue number (in the topology) 
        to which the MTSSL spin label 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. The user can decide to use either N1 ``--no-useNOelectron`` 
        or the geometric midpointis N1 and O1  ``--useNOelectron``  to calculate 
        the distances. Two libraries are offered: `MTSSL 298K 2011` or 
        `MTSSL 298K 2015` (default) by defining the option ``--libname``. 
        For further explanations see the ``--help`` option.
        
        
        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
        .. -----
        
        .. _`RotamerConvolveMD documentation`:
           https://www.mdanalysis.org/RotamerConvolveMD
        .. _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
        .. _pip: https://pip.pypa.io/
        
        .. Badges
        .. ------
        .. |docs| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg
           :alt: Documentation (latest release)
           :target: `RotamerConvolveMD documentation`_
        
           
        .. 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. Stelzl, 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
        
        
        
Keywords: science proteins
Platform: UNKNOWN
Classifier: Development Status :: 7 - Inactive
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires: numpy (>=1.6)
Requires: MDAnalysis (>=0.16.2)
Provides: rotcon
Description-Content-Type: text/x-rst
