.. -*- coding: utf-8 -*- .. RotamerConvolve documentation master file, created by sphinx-quickstart on Thu Oct 5 15:44:48 2017. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. =================== RotamerConvolveMD =================== :Release: |release| :Date: |today| 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 protein 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. When using this code please cite [Stelzl2014]_ and [Polyhach2011]_. This package contains MTSL :ref:`rotamer-libraries` provided by `Gunnar Jeschke`_ (published under the GPL with his permission). If you have questions or problems installing the package then ask on the MDAnalysis user mailing list: https://groups.google.com/group/mdnalysis-discussion Source code is available from https://github.com/MDAnalysis/RotamerConvolveMD under the open source GNU General Public License, version 2. .. _Gunnar Jeschke: http://www.epr.ethz.ch/ .. Content (in sidebar) .. ==================== .. toctree:: :maxdepth: 4 :hidden: installation background libraries usage References ========== .. [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`_. https://www.mdanalysis.org .. _`10.1002/jcc.21787`: https://doi.org/10.1002/jcc.21787 .. [Gowers2016] R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domański, S. Buchoux, I. M. Kenney, and O. Beckstein. `MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations`_. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 102 – 109, Austin, TX, 2016. SciPy. .. _`MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations`: http://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html .. [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`: https://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`: https://doi.org/10.1016/j.jmb.2013.10.024 .. [Fowler2015] P. W. Fowler, M. Orwick-Rydmark, S. Radestock, N. Solcan, P. M. Dijkman, J. A. Lyons, J. Kwok, M. Caffrey, A. Watts, L. R. Forrest, and S. Newstead. Gating topology of the proton-coupled oligopeptide symporters. Structure, 23:290–301, 2015. doi:`10.1016/j.str.2014.12.012`_ .. _`10.1016/j.str.2014.12.012`: https://doi.org/10.1016/j.str.2014.12.012 Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search`