New Chimera Fitting Capabilities

Tom Goddard
June 27, 2011

Demonstration of new tools in UCSF Chimera software for fitting atomic models in electron microscopy maps.

Note: Demo needs internet connection to use web services: Fetch PDB/EMDB, BLAST, Modeller and SAXS.

What can go wrong in fitting?

Will show three new fitting tools that help with packing molecules in low resolution maps.

Will show ways to examine the range of conformations available from x-ray and nmr models.

Comparing fits of a map to small-angle x-ray scattering (SAXS) profiles can indicate if the map shape is wrong.

Demonstration 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.

Demonstration Outline

Finding alpha crystallin PDB models

Use white background, silhouette edges and glossy lighting.

Homology modeling

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

Small-angle x-ray scattering profiles

Published SAXS dimer result, Strelkov lab

SAXS fit of alphaB crystallin dimers with different beta-sheet registrations from

Baranova EV, Weeks SD, Beelen S, Bukach OV, Gusev NB, Strelkov SV.
Three-Dimensional Structure of α-Crystallin Domain Dimers of Human Small Heat Shock Proteins HSPB1 and HSPB6.
J Mol Biol. 2011 May 30.

Fig. 5 from Strelkov lab paper. "Fitting of the obtained SAXS data with atomic models. (a) Scattering curves of reduced B1α, oxidized B1α and B6α were fitted with the coordinates of the ACD dimer of αB-crystallin (PDB ID: 2WJ7) using CRYSOL.53 For clarity, the curves are offset in vertical direction. Experimental and calculated scattering curves are shown in black and red, respectively. The calculated quality of fit, χ2, is given. (b) Scattering curve of the reduced B1α sample was fitted with various dimeric ACD structures: bovine αB-crystallin (API), human αB-crystallin (APII), rat HSPB6 (APIII) and human αB-crystallin determined by NMR (NMR APII). (c) Ribbon diagrams of the atomic models used for fitting in (b). The orientation of the right-hand ACD is the same for all models."


  • Chimera Team
  • Eric Pettersen - Sequence and structure analysis.
  • Elaine Meng - Email help, documentation and tutorials.
  • YZ Yang Zheng - Homology modeling, SAXS.
  • Greg Couch - OpenGL graphics.
  • Darren Weber - Animation.
  • Conrad Huang - Web services and project leader.
  • Tom Ferrin - Head of lab.
  • Collaborators
  • Dina Schneidman - SAXS
  • Keren Lasker - MultiFit
  • Ben Webb - Modeller
  • Andrej Sali
  • Stephen Weeks - SAXS data
  • Sergei Strelkov