Volume Data Display in Chimera

Chimera tutorial
USCF Mission Bay Library
July 15, 9:00 - 11:00 AM

Kinds of Volume Data Shown by Chimera

Molecular orbitals

X-ray density map

Electrostatic potential

Water occupancy

DOCK scoring grids

Electron microscope single particle reconstructions

Electron microscope tomography

3-d light microscopy (wide-field, confocal, ...)



Display x-ray density map

Contour level


volume dialog

high contour level, disulfides

low contour level, data bounds

Where is the conotoxin?

Tyrosine residue in density.

Measure and Color Blobs.

Colored protein copies.

Unobstructed view: clipping and capping

Side view dialog

Clipping density in front.

Surface capping dialog.

Covering holes in surface.

Unobstructed view: per-model clipping

Per-model clipping dialog.

Slab clipping.

Unobstructed view: subregions

Subregion selection panel.

Green outline box.

After pressing Crop.

Unobstructed view: zones

Atomic model (PDB file).

Zone panel.

Zone around chain A.

Fitting residues

Serine 4, chain A.

Rotamers dialog.

Second best orientation.

Atoms outside density

Values at atom positions.

Render by attribute dialog.

Atoms colored by density.

Color chooser.

Electron microscopy fitting

Microtubule map and tubulin dimer.

Fit in map dialog.

Fit tubulin including simulated map.

Electron microscopy markers and coloring

Volume tracer dialog.

Markers for tubulin monomers.

Colored map.

Color zone dialog.

EM tomography plane display and masking

Human cytotoxic T-cell.

Volume planes panel.

Traced objects from IMOD.

Masked vesicle.

Self-Guided Exercises