Modeling of CryoEM Map Workshop - Houston, Jan. 14-17, 2010

TCB Hands-on Workshop in Urbana

Tutorials

Below is a list of tutorials used at the workshop.
  • Using VMD (html) (pdf, 1.4M) (required tutorial files [.tar.gz, 44.9M], [.zip, 44.9M], individual files)
    Participants build an image of ubiquitin while becoming familiar with basic VMD commands. Additionally, participants learn how to look for interesting structural properties of proteins using VMD. Tutorial works on Windows, Mac, and Unix/Linux platforms.

  • NAMD Tutorial
    (html for Unix/Mac) (pdf for Unix/Mac, 8.0M)
    (html for Windows) (pdf for Windows, 6.5M)
    (required tutorial files (all platforms) [.tar.gz, 148M], [.zip, 148M], individual files (all platforms))
    Participants learn how to use NAMD to set up basic molecular dynamics simulations, and to understand typical NAMD input and output files, with an emphasis on such files for protein energy minimization and equilibration in water. Tutorial versions available for Windows, or Mac and Unix/Linux platforms.

  • Membrane Proteins Tutorial (pdf, 1.0M) (required tutorial files: reduced version [.tar.gz, 10.2M]; full version, [.tar.gz, 508M]*)
    Step by step tutorial for setting up and running molecular dynamics simulations of membrane proteins. Requires VMD, NAMD, and Solvate. Tutorial works on Unix/Linux platform. *Note: download of full version of files limited by bandwidth availability.

  • Molecular Dynamics Flexible Fitting (MDFF) (html) (pdf, 1.1M) (required tutorial files [.tar.gz, 29.7M] [.zip, 29.7M], individual files)
    This tutorial describes how to flexibly fit atomic structures into density maps using the MDFF method. This method can be used to obtain atomic models of macromolecular complexes by combining X-ray structures and cry-electron microscopy maps. Requires VMD and NAMD. Tutorial works on Windows, Mac, and Unix/Linux platforms.