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, ...)


Orientation

Demonstration

Display x-ray density map

Contour level


1a0m.omap

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

Exercises