UCSF Chimera Video Documentation

Tom Goddard, Andrew Ling
Updated October 22, 2012

Molecular Assembly Display and Analysis

Microtubule symmetry. Helix symmetry. Cage builder. Measure domain rotation.
Virus crystal contacts. Find surface residues. Virus capsid display.

Density Map Display and Measurement

Local correlation. Map time series.
Spherical clipping. Report map positions. Icosahedral wedge. Unroll cylinder.
Show icosahedral cage. Map values at atom positions. Cavity volume. Oblique slicing.
Measure distances between surfaces. Measure filament diameter. Virus shell distance measurement. Measuring length of segmented bacteria.

Segmenting and Fitting Volume Data

Mask to traced surface. Smooth mask boundary.
MultiFit asymmetric fitting. MultiFit cyclic symmetry. Sequential fitting. Symmetric fitting.
Global fitting. Global and symmetric fitting. Rous sarcoma virus tutorial. Slice images of segmented objects.
Extract rotated box. Placing markers on vesicles in a density. Segmenting a density map and fitting a molecule. Segmenting a density map using the mouse.

Molecular Modeling

Building a homology model.

Movie Recording

Smooth transition between two scenes. Fly-through animation.


Aligning and morphing two maps. Morphing between two density maps. How to align two protein chains and morph one into another.
Download video (Quicktime format, 218 Mb).

Electrostatic Potential

Inspecting electrostatic potential values. How to view electrostatic potential and standard residue charges.
Download video (Quicktime format, 87 Mb).

Fitting a Molecule in a Density Map

How to fit a tubulin monomer into a microtubule map. Download video (Quicktime format, 112 Mbytes). Fitting a second copy of tubulin. Download video (Quicktime format, 62 Mbytes). Checking the correlation coefficient. Download video (Quicktime format, 57 Mbytes).

Viral Outbreak HHMI DVD

Part 1: How to use the Chimera
HHMI Virus Viewer.
Part 2: Finding virus models on the web. Part 3: Exploring a virus in atomic detail.