SI2007 Molecular Visualization and Virtual Screening

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General Information

This track is for students, postdocs, programmers and researchers interested in Molecular Graphics and Modeling and programmers interested in adapting Vision to any other scientific field.

Time: 2 to 5 pm

Location: TSRI Training Lab, Room 310, 3377 N. Torrey Pines Ct

Prerequisites: No prior knowledge of Python, VISION or PMV is required. If you are planing to bring your own laptop, please install mgltools.


  • Tuesday, July 31, Python Molecular Viewer and Visualization Techniques
    Instructors: Michel Sanner, Ph.D. & Sargis Dallakyan, Ph.D.
    Attendees will learn how to use PMV for visualizing molecules in various ways and produce publication-quality images. The commands covered include loading molecules and displaying them using various representations, computing molecular surfaces and secondary structure representations, selecting subsets of atoms for coloring and labeling and using APBS to compute and visualize electrostatic potentials.
    During this course we will introduce some of the underlying design principles and we will point out the main differences with other molecular visualization tools. Use of PMV to access distributed computing resources will also be included. Read more
    Python Molecular Viewer Step-by-step tutorial
  • Wednesday, August 1, The Vision Programming Environment
    Instructors: Michel Sanner, Ph.D. & Guillaume Vareille, Research Programmer
    Attendees will learn how to use VISION, a visual/graphic programming tool to create networks of computational nodes. VISION can be used on its own or in conjunction with PMV. VISION is design to perform scientific calculation The nodes libraries developed by Michel SANNER covers essentially chemistry and biochemistry. VISION delivers publication-quality images. All the aspect of VISION programming will be covered.
    Vision tutorial
  • Thursday, Aug 2, Using AutoDock with AutoDockTools
    Instructors: Ruth Huey, Ph.D. & Garrett M. Morris, M.A. (Oxon.), D.Phil. (Oxon.)
    This tutorial is a prerequisite for the "Using AutoDock for Virtual Screening" tutorial. It introduces the graphical user interface of AutoDockTools (ADT), and teaches:
    how to set up the protein for AutoGrid
    how to set up and launch AutoGrid calculations of atomic affinity maps, electrostatic potential map, and desolvation map
    how to set up the ligand for AutoDock
    how to setup AutoDock docking calculations with flexible ligands;
    how to analyse the docking results from AutoDock calculations.
    Using AutoDock with AutoDockTools Step-by-step tutorial
    Slides from Garrett M. Morris' presentation

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