.. -*- coding: utf-8 -*- Protein visualization and analysis with VMD =========================================== .. Note:: Short URL for this page: https://goo.gl/nGTVXB This tutorial provides a short introduction to basic use of the VMD_ ("Visual Molecular Dynamics") software to visualize and analyze proteins and molecular dynamics trajectories. It is part of the ASU_ course `PHY 542/NAN 542 — Topics in Biophysics I`_. For background on using VMD_, look at [Hsin2008]_ and the official `VMD tutorial`_. We will use data from the `Protein Databank`_ and [Beckstein2009]_. Basics of protein structure are illustrated in [BrandenTooze]_ and in the lecture notes. Contents ======== We are going to work through the individual sections in order. Use the navigation links in menu bar to move forward and backwards. .. toctree:: :maxdepth: 1 proteinbasics structure/index rendering dynamics/index movies Learning Objectives =================== - basic understanding of protein structure - familiarize with a molecular graphics program (VMD) - loading of static structures and dynamics trajectories - viewing a molecule (mouse, view modes) - representations - selections - making images - basic analysis - use of RMSFitting tools References ========== .. _VMD: http://www.ks.uiuc.edu/Research/vmd .. _VMD tutorial: http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/ .. _1AKE: http://dx.doi.org/10.2210/pdb1ake/pdb .. _ASU: http://asu.edu .. _`PHY 542/NAN 542 — Topics in Biophysics I`: https://becksteinlab.physics.asu.edu/learning/40/phy542-nan542-phy498-topics-in-biophysics-i .. _Protein Databank: http://www.rcsb.org/pdb .. [BrandenTooze] C. Branden and J. Tooze. Introduction to Protein Structure. 2nd ed, 1999, Garland Publishing, New York. .. [Hsin2008] J. Hsin, A. Arkhipov, Y. Yin, J. E. Stone, and K. Schulten. Using VMD: An Introductory Tutorial, volume 24, chapter 5.7, pages 5.7.1--5.7.48. John Wiley & Sons, Inc., 2008. URL http://dx.doi.org/10.1002/0471250953.bi0507s24. .. [Beckstein2009] O Beckstein. EJ Denning, JR Perilla, and TB Woolf. Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open/Closed Transitions. J Mol Biol 394 (2009), 160--176. http://dx.doi.org/10.1016/j.jmb.2009.09.009 Indices and tables ================== * :ref:`genindex` * :ref:`search`