{
    "info": {
        "author": "Philip W. Fowler",
        "author_email": "philip.fowler@ndm.ox.ac.uk",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 7 - Inactive",
            "Environment :: Console",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v2 (GPLv2)",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Chemistry"
        ],
        "description": ".. -*- mode: rst; coding: utf-8 -*-\n\n======================================\n MTSL Rotamer fitting to trajectories\n======================================\n\n:Author:    Philip W Fowler, Oliver Beckstein, Katrin Reichel, and AUTHORS_\n:Year:      2013\n:Licence:   GNU Public Licence, version 2 (or higher)\n:Copyright: \u00a9 2013 Philip W Fowler, Oliver Beckstein,\n            \u00a9 2014\u20132017 AUTHORS_\n:Citation:  LS Stelzl, PW Fowler, MSP Sansom, O Beckstein. J Mol Biol\n            426 (2014), 735-751. doi: 10.1016/j.jmb.2013.10.024\n:Documentation: |docs|\n\n.. _AUTHORS:\n   https://raw.githubusercontent.com/MDAnalysis/RotamerConvolveMD/master/AUTHORS\n\nThis package contains the *MTSL rotamer library R1A_298K (2011)* and\nan *updated MTSL rotamer library R1A_298K (2015)* provided by `Gunnar\nJeschke`_, which is also published under the GPL with his\npermission. The updated rotamer library was sent by `Gunnar Jeschke`_\nafter personal discussion.\n\nSummary\n=======\n\nThis package analyses molecular dynamics trajectories or\nconformational ensembles in terms of spin-label distances as probed in\ndouble electron-electron resonance (DEER) experiments and spin-label\nto amide protin distances as probed in paramagnetic relaxation\nenhancement (PRE) experiments. The spin labels are fitted on\ntrajectories and the spin label mobility is taken into account using a\nrotamer library.\n\nFor further details see the `RotamerConvolveMD documentation`_.\n\n\n\nBackground\n==========\n\nSite-directed spin labeling (SDSL) is a common technique to\ninvestigate structure and dynamics of macromolecular\nsystems. Covalentry attached spin labels are introduced to the system\nand induce electron spin resonance.  Double electron electron spin\nresonance (DEER) is an EPR technique for measuring distances between\ntwo spin labels that have been covalently attached to a protein. Two\ncysteine residues are introduced into the protein and subsequently\nlabelled. Paramagnetic relaxation enhancement (PRE) is an NMR\ntechnique for measuring distances between a spin label and the amide\nprotons of the protein backbone. One cysteine residue is introduced at\nthe position of the label The positions are chosen to report on the\nexpected conformational change. A commonly used spin label is\n(1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl)-methanethiosulfonate\n(MTSL). MTSL has a linker with five rotatable bonds and is therefore\nvery flexible. The distance distributions between the two spin labels\n(DEER) or one spin label and the amide protons are measured by\nexperiments are typically broad and often multi-modal. The\ndistributions are therefore a convolution of the flexibility of the\nMTSL spin label and the conformational spread of the proteins in the\nsample. To ensure that we compared like with like we developed a\nmethod that\n\n1. maps rotamer libraries of the MTSL spin label onto each position,\n\n2. discards those rotamers that sterically clash with the protein\n   (typically distances <2 \u00c5) and\n\n3. calculates all (weighted) distance pairs between the remaining\n   rotamers and \n\n4. thereby estimates a distance distribution for that structure. \n\nThe code was written in Python using the MDAnalysis_ library\n[Michaud-Agrawal2011]_ and a published rotamer library for MTSL\n[Polyhach2011]_. It is available for download from the MDAnalysis\nwebsite, https://github.com/MDAnalysis/RotamerConvolveMD .\n\nOur approach improves upon the existing method [Polyhach2011]_ by\nincreasing computational efficiency and implementing, via the\nMDAnalysis library, analysis of ensembles of hundreds of structures,\nwhich allowed us to estimate distance distributions for entire\nsimulation trajectories. In the case of PRE measurements, it enables \nthe user to calculate back the transverse relaxation enhancement \nto compare raw data without calculating the distances based on the\nexperiment.\n\nIn the case of MTSL, the distances are determined by considering the position of the free electron\nlocated between nitrogen (N1) and (O1).\n\nExamples of the application of this approach can be found in\n[Stelzl2014]_.\n\n\nInstallation\n============\n\nTypically, install the package with pip_ ::\n\n   pip install RotamerConvolveMD\n\n(see also the file ``INSTALL.rst``)\n\nThis will automatically install MDAnalysis and other dependencies. If\nproblems arise, try installing MDAnalysis first (see\nhttp://www.mdanalysis.org for help).\n\nAnalysis is performed with the script ``convolve-mtss-rotamers.py`` \n(DEER) or ``convolve-mtss-rotamers_pre.py`` (PRE), \nwhich will have been installed in your ``bin`` directory. You might\nhave to add the bin directory to your ``PATH``. Consult your Python\ndocumentation for the details although often this will be\n``~/.local/bin`` (for a ``--user`` installation or ``/usr/local/bin``\nfor site-wide installation). \n\n\nUsage\n=====\n\nDEER\n----\n\nAnalysis for standard DEER experiments with MTSL spin labels is\nperformed with the script ``convolve-mtss-rotamers.py``. It takes as\ninput\n\n* a topology or structure file (psf, gro, pdb, ... any `topology\n  format`_ recognized by mdanalysis)\n* a trajectory (dcd, xtc, trr, ... any `trajectory format`_ that\n  mdanalysis can read)\n\na typical invocation::\n\n    convolve-mtss-rotamers.py \\\n        --resid 47 330  \\\n        --histogramBins 0 80 1  \\\n        --clashDistance 2.2  \\\n        --output \"dat/peptso-xrd\" \\\n        --plotname \"dat/peptso-xrd.pdf\" \\\n        --outputRawDistances \"dat/peptso-xrd\" \\\n        --dcdfilename \"dcd/peptso-xrd\" \\\n        --dcdfilenameNoClashes \"dcd/peptso-xrd\" \\\n        --useNOelectron \\\n        --libname \"MTSSL 298K 2015\" \\\n        peptso.gro peptso.xtc\n\nIt loads the MD trajectory from the topology ``peptso.gro`` and the\ntrajectory ``peptso.xtc``. The ``--resid`` pair is required and\ndenotes the residue numbers (in the topology) to which the MTSSL spin\nlabels would be attached. Rotamers that overlap with protein atoms as\nmeasured by an atom-atom distance smaller than the ``--clashDistance``\nwill be discarded and not counted in the distance calculations. \nThe user can decide to use either N1 ``--no-useNOelectron`` or the \ngeometric midpointis N1 and O1  ``--useNOelectron``  to calculate \nthe distances. Two libraries are offered: `MTSSL 298K 2011` or \n`MTSSL 298K 2015` (default) by defining the option ``--libname``. \nFor further explanations see the ``--help`` option.\n\nFor an example, see ``doc/example`` in the source distribution. The\nexample can also be run to test the installation as reference output\nis provided.\n\n\nPRE\n---\n\nAnalysis for standard PRE experiments with MTSL spin label is performed \nwith the script ``convolve-mtss-rotamers_pre.py``. Similar to the \nanalysis of DEER experiments, it takes as inputs:\n\n* a topology or structure file (psf, gro, pdb, ... any `topology\n  format`_ recognized by mdanalysis)\n* a trajectory (dcd, xtc, trr, ... any `trajectory format`_ that\n  mdanalysis can read)\n\na typical invocation::\n\n    convolve-mtss-rotamers_pre.py \\\n        --resid 47  \\\n        --clashDistance 2.2  \\\n        --plotname \"dat/peptso-xrd-47.pdf\" \\\n        --outputRawDistances \"dat/peptso-xrd\" \\\n        --dcdfilenameAll \"dcd/peptso-xrd\" \\\n        --dcdfilenameNoClashes \"dcd/peptso-xrd\" \\\n        --useNOelectron \\\n        --libname \"MTSSL 298K 2015\" \\\n        peptso.gro peptso.xtc \n\nThe ``--resid`` is required and denotes the residue number (in the topology) \nto which the MTSSL spin label would be attached. Rotamers that overlap \nwith protein atoms as measured by an atom-atom distance smaller than \nthe ``--clashDistance`` will be discarded and not counted in the distance \ncalculations. The user can decide to use either N1 ``--no-useNOelectron`` \nor the geometric midpointis N1 and O1  ``--useNOelectron``  to calculate \nthe distances. Two libraries are offered: `MTSSL 298K 2011` or \n`MTSSL 298K 2015` (default) by defining the option ``--libname``. \nFor further explanations see the ``--help`` option.\n\n\nHelp\n====\n\nIf you have questions or problems installing the package then ask on\nthe MDAnalysis user mailing list:\nhttp://groups.google.com/group/mdnalysis-discussion\n\n\nReferences\n==========\n\n.. Links\n.. -----\n\n.. _`RotamerConvolveMD documentation`:\n   https://www.mdanalysis.org/RotamerConvolveMD\n.. _MDAnalysis: http://www.mdanalysis.org\n.. _Gunnar Jeschke: http://www.epr.ethz.ch/\n.. _topology format: \n   https://pythonhosted.org/MDAnalysis/documentation_pages/topology/init.html#supported-topology-formats\n.. _trajectory format:\n   https://pythonhosted.org/MDAnalysis/documentation_pages/coordinates/init.html#id1\n.. _pip: https://pip.pypa.io/\n\n.. Badges\n.. ------\n.. |docs| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg\n   :alt: Documentation (latest release)\n   :target: `RotamerConvolveMD documentation`_\n\n\n.. Articles\n.. --------\n\n.. [Michaud-Agrawal2011] N. Michaud-Agrawal, E. J. Denning,\n   T. B. Woolf, and O. Beckstein. MDAnalysis: A toolkit for the\n   analysis of molecular dynamics simulations. J Comp Chem,\n   32:2319-2327, 2011. doi:`10.1002/jcc.21787`_. http://www.mdanalysis.org\n\n.. _`10.1002/jcc.21787`: http://doi.org/10.1002/jcc.21787\n\n.. [Polyhach2011] Y. Polyhach, E. Bordignon, and G. Jeschke. Rotamer\n   libraries of spin labelled cysteines for protein\n   studies. Phys. Chem. Chem. Phys., 13:2356-2366, 2011. \n   doi: `10.1039/C0CP01865A`_.\n\n.. _`10.1039/C0CP01865A`: http://dx.doi.org/10.1039/C0CP01865A\n\n.. [Stelzl2014] L. S. Stelzl, P. W. Fowler, M. S. P. Sansom, and\n   O. Beckstein. Flexible gates generate occluded intermediates in the\n   transport cycle of LacY. J Mol Biol, 426:735-751, 2013. \n   doi: `10.1016/j.jmb.2013.10.024`_ \n\n.. _`10.1016/j.jmb.2013.10.024`: http://dx.doi.org/10.1016/j.jmb.2013.10.024\n\n\n\n\n",
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