New Chimera Fitting Capabilities

Tom Goddard
3D EM Gordon Conference
June 27, 2011


Example system: Alpha Crystallin

Alpha crystallin is a molecular chaperone that prevents protein aggregation. There are two forms A and B with 60% sequence identity with the A form found only in the vertebrate eye lens. It is about 40 percent of the protein in the human eye lens and prevents crystallization of the other proteins in the lens. The EM map we will look at is of the B form found it brain, heart and muscle tissue and has a role in diseases such as Alzheimer's, Parkinson's and multiple sclerosis where protein aggregation occurs.

Alpha crystallin forms oligomers of variable size, the map we will look at consisting of 24 copies, negative stain, 20 Angstrom resolution (FSC 0.5) from Sevil Weinkauf and Johannes Buchner groups, EM Databank 1776.

Demonstration Outline

Finding alpha crystallin PDB models

Use white background, silhouette edges and glossy lighting.

Binding Interfaces - Crystal Unit Cell

Fitting in EM map, global search

Assigning and Using Map Symmetry

Avoiding fitting clashes: sequential fitting

Avoiding fitting clashes: symmetric fitting

Chimera Team

  • Darren Weber - Animation.
  • Eric Pettersen - Sequence and structure analysis.
  • Elaine Meng - Email help, documentation and tutorials.
  • Conrad Huang - Web services and project leader.
  • Tom Goddard - Electron microscopy.
  • Tom Ferrin - Head of lab.
  • Greg Couch - OpenGL graphics.
  • YZ Yang Zheng - Homology modeling, SAXS.

The new fitting methods are in the Chimera daily builds and video demonstrations are on the Chimera web site.