Volume Visualization using Chimera

Tom Goddard
November 8, 2001
NCRR site visit

All images on this page ©2004 The Regents, University of California; all rights reserved.


Large Range of Data Resolutions

Crystallographic density

Electrostatic potential

Water occupancy map (1A)

Electron cryo-microscopy (7A)

Electron microscopy (300A)

Light microscopy (2000A)

Barcoded Chromosomes

  • Arrangement of chromosomes in the cell nucleus.
  • Collaboration with Mike Lowenstein in John Sedat's lab, UCSF.
  • 3D light microscope images of chromosome 2L in Drosophila nuclei.
  • Can determine whether specific stretches of DNA are attached to the nuclear envelope.
  • Can study spatial arrangements characteristic of differentiated cell types.
  • Can study relation between gene transcription and spatial arrangement.

Tracing Chromosomes

  • Drosophila chromosome 2L has 13 fluorescently labeled segments using 3 fluorophors.
  • Trace path of chromosome by finding expected sequence of color spots in light microscope data.
  • Different colors provide improved resolution
  • Colors allow correct interpretation when spots are missing
  • Prior to Chimera, tracing was done by flipping through a stack of 2 dimensional images and typing observed sequence of spot id numbers into a file.
  • DAPI stain in light microscope images illuminates all DNA.
  • Nuclear envelope can be shown as boundary of DAPI stained region.

Low Resolution Protein Structures from
Electron Cryo-Microscopy

  • Rice dwarf virus capsid protein structure determined
  • 7 angstrom resolution is sufficient to model alpha helices and beta sheets.
  • Single particle cryo-EM can handle large complexes and does not require crystalization.
  • Useful for determining protein folds
  • Can determine relative orientations of components of complexes
  • Work is done by Wah Chiu's group at Baylor College of Medicine, National Center for Macromolecular Imaging.
  • Alpha helices are found in density map by program helixhunter
  • Helixhunter developed by Wen Jiang, Matthew Baker, in Wah Chiu's lab.
  • Display predicted helices superimposed with EM data.

Tracing Connections between Helices

  • Interactively trace turns connecting helices.
  • Goal is to find correct helix order, not exact turn structure.
  • Helices predicted from amino acid sequence can be matched to those found in density map.
  • Without Chimera, Wah's group did turn tracing on 2 dimensional images in Photoshop.
  • Rice dwarf virus analysis was completed 5 months ago at start of our collaboration.
  • Chimera not used for results published in October issue of Nature Structural Biology.
  • Homology to known crystal structure of Bluetongue virus P7 capsid protein used in tracing turns.

Strengths of Chimera Volume Visualization

Future Development

How to Depict Macromodels

Analyzing Macromodels: An Example

Macromodel Development Objectives

Volume Time Series

Water Dynamics around Collagen

Chromosome Dynamics during the Cell Cycle