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HIV Dataset Tutorial

In this tutorial, we will work on the HIV immature capsid virus-like particles (VLPs) dataset found in EMPIAR-10164. The goals for this tutorial include:

  • Setting up a TOMOMAN project directory
  • Running TOMOMAN jobs locally
  • Performing preprocessing using TOMOMAN
  • Automated tilt series alignment in AreTomo
  • 3D-CTF corrected tomogram reconstruction with NovaCTF
  • Manually picking spherical particles in Chimera using the Pick Particle tool
  • Generating oversampled initial particle positions on spherical surfaces
  • Setting up a STOPGAP project directory
  • Running STOPGAP jobs locally
  • Extracting subtomograms using STOPGAP
  • Subtomogram alignment and averaging in STOPGAP
  • Visualizing particle positions in Chimera using the Place Objects tool
  • Generating a de novo structure from a single VLP at 8x binning
  • Expanding the dataset to all VLPs in the 8x-binned tomogram
  • Rescaling the motivelists for processing 4x-binned data

External Packages

During this tutorial we will be using a number of other software packages. These include: