TUTORIAL B6

Using Sirius with AMBER

By Sasha Buzko

This tutorial is intended to provide an introduction to using Sirius for visualization of data produced by AMBER. It describes loading various MD trajectory data formats, as well as manipulation of the displayed data. Since Sirius is a full-featured desktop environment, a complete discussion of its capabilities is beyond the scope of this tutorial. For a full description, please refer to Sirius web site.

Introduction

Sirius (http://sirius.sdsc.edu) is a recently released desktop software designed for a variety of visualization and data manipulation tasks, including multiple modes of visual representation, building of structures from fragments, structure editing, visualization of molecular dynamics trajectories, creation of high- quality graphics, and much more. Sirius is being developed at San Diego Supercomputer Center, and its development is funded in part by the National Science Foundation. It is available free of charge to academic and non-profit institutions and can be downloaded from the above link.

As a part of its feature set, Sirius provides an advanced molecular dynamics visualization module capable of displaying output produced by the AMBER software suite. In addition to basic loading and playback, it is possible to open multiple sequential trajectory files, compute RMSD graphs on the fly using a user-defined set of atoms, recompute secondary structure during a folding simulation, or load compressed output or coordinate files.

Sirius is available for Windows, MacOS X (10.3+) and Linux. Application behavior is identical on all three platforms, except that the current version (1.1) does not support ray-traced image output for Mac. For a more detailed description, please refer to Sirius tutorials, as well as application help.

For the purposes of this tutorial, it will be assumed that you are using Linux.

This tutorial consists of  nine sections:

  1. section1.htm : Sirius installation and initial setup

  2. section2.htm : Loading structures from PDB and local files

  3. section3.htm : Opening MD visualization module and loading AMBER trajectory data

  4. section4.htm : Working with AMBER output files

  5. section5.htm : Computing RMSD

  6. section6.htm : Advanced visualization options: displaying solvent, view centering, secondary structure update

  7. section7.htm : Buffered trajectory loading and saving individual frames

  8. section8.htm : Exporting a video of the loaded trajectory and ray-traced frame snapshots

CLICK HERE TO GO TO SECTION 1

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