Alignment Viewer

The Multalign Viewer extension displays multiple sequence alignments, calculates and shows a consensus sequence and conservation histogram, and allows regions to be defined and colored. Structures opened in Chimera are automatically associated with a matching sequence. Structures can be superimposed based on the sequence alignment, and actual/predicted secondary structure features can be depicted on the alignment. When a region is defined by dragging within the sequence, the corresponding residues of the structure are highlighted. The color swatches behind the sequence names match the corresponding structures.

Morphing

Different conformations and even different proteins can be compared by morphing from one structure to another. Users can specify the method of coordinate interpolation and how many intermediate structures should be generated. The result is displayed in Chimera's trajectory viewer, MD Movie. The morph can then be saved in coordinate form or recorded as an animation.

Molecular Graphics

• stick, ball-and-stick, CPK, ribbon, pipe-and-plank, and nucleotide display styles
• molecular surfaces
• highly intuitive rotation, translation, and scaling with the mouse
• Side View for adjusting clipping planes and scaling
• interactive color editing in various color spaces (RGB, CMYK, etc.) with transparency
• ability to save high-resolution images for presentation and publication
• stereo (side-by-side and time-sequential)

Chemical Knowledge

• determination of atom types in arbitrary molecules, including non-standard residues
• ability to add hydrogen atoms
• high-quality hydrogen bond identification
• selection of atoms/bonds by element, atom type, functional group, amino acid category
• interactive bond rotation, distance and angle measurements

Molecular Dynamics / Lenses

Chimera can display molecular dynamics trajectories in a variety of formats: AMBER, CHARMM, GROMACS, GROMOS, MMTK, NAMD, PDB, and X-PLOR. All normal Chimera analysis and display capabilities are available with trajectories. One such capability is to place lenses on the screen: rectangular regions containing markedly different display properties. The accompanying image shows one trajectory frame of a buckytube immersed in water. A lens has been placed over the center of the buckytube to reveal the hydrogen-bonded chain of waters in the center of the tube, along with their residue numbers. The simulation was done with polarizable molecular dynamics using the Amber8 Sander module, and provided courtesy of J. Caldwell.

Volume Data

Chimera's Volume Viewer displays three-dimensional electron and light microscope data, X-ray density maps, electrostatic potential and other volumetric data. Contour surfaces, meshes and volumetric display styles are provided and thresholds can be changed interactively. Maps can be colored, sliced, segmented, and modifications can be saved. Markers can be placed and structures can be traced. The accompanying image shows a density map of Kelp fly virus from electron microscopy colored radially and with an octant cut out.

Multiscale Models

The Multiscale Models extension allows Chimera to display large complexes such as virus capsids, ribosomes, and chromatin. It displays the quaternary structure of PDB models and allows subunits to be selected and shown in atomic detail. Matrices are read from PDB files that specify the biological unit. Crystallographic packing can also be shown.

Screening Docked Molecules

The program DOCK calculates possible binding orientations, given the structures of "ligand" and "receptor" molecules. Typically, a large database of small molecule structures is searched for compounds that may bind the receptor. The Chimera extension ViewDock facilitates interactive selection of promising compounds from the output of DOCK. The molecules can be viewed in the context of the binding site and optionally, screened by number of hydrogen bonds to the receptor. The Dock Prep extension prepares a receptor for input to a docking program by adding hydrogens, assigning partial charges, and performing other related tasks.

User-Driven Analysis

Users can easily import structure-related data into Chimera in the form of attributes, or values associated with atoms, residues, or models. The data can be imported with Define Attribute and then represented visually with color ranges, atomic radii, or "worm" thickness. Such data can also be manipulated programmatically in Chimera, and in fact Chimera was designed with extensibility and programmability in mind. It is largely implemented in Python, with certain features coded in C++ for efficiency. Python is an easy-to-learn interpreted language with object-oriented features. All of Chimera's functionality is accessible through Python and users can implement their own algorithms and extensions without any Chimera code changes, so any such custom extensions will continue to work across Chimera releases. Many programming examples are provided to assist extension writers.

Rotamers

Amino acid sidechains adopt different conformational states, or rotamers. Rotamers from the Dunbrack backbone-dependent library or the Richardson "penultimate" library can be viewed, evaluated, and incorporated into structures with the Rotamers tool. A residue can be changed into a different conformation of the same type of amino acid or mutated into a different type. Rotamer torsion angles and library probability values are listed in a dialog, along with (optionally) hydrogen bonds, clashes, and agreement with electron density data. Only rotamers chosen in the list are displayed. When a single rotamer is chosen, it can be incorporated into the structure. The image includes 2D labels.

Sequence Viewer

The Sequence tool shows the sequence of each chain in a structure – the example contains both protein and DNA. In the sequence, protein helix and strand segments are colored gold and green, respectively, and specific patterns can be identified. Sequence and structure are linked:
   • mousing over a residue in the sequence shows its structure residue number
   • selecting in the sequence selects residues in the structure and vice versa
See also the sequence alignment viewer.

Morphing Density Maps

Related density maps can be compared by morphing from one to the other. Several intermediate maps are generated by interpolating between the starting and ending maps. The morph can be viewed interactively and recorded as a movie. The contour level can be adjusted automatically to keep the enclosed volume constant throughout the morph, and other aspects of map display can be adjusted with Volume Viewer.

Volume Plane Display

Volume data can be shown a single plane (or slab) at a time with the Planes feature in Volume Viewer. Plane display can be set to oscillate along the data X, Y, or Z axis, or the plane location can be specified interactively with a slider.

Topography

Values in a plane of volume data can be shown as heights normal to the plane (a topographic map). When a single plane is displayed with Volume Viewer, the command topography will plot the values as heights in a surface.

Coloring by Density

A surface can be colored by density or other volume data. In the image, the surface is clipped and capped, and only the cap is colored by density. Different coloring schemes can be applied.

Radial Coloring

A surface can be colored radially, that is, by distance from a user-specified point. Additional options include coloring by distance from an axis or a plane. Different coloring schemes can be applied.

Coloring by Conservation

A structure can be colored by attribute values such as conservation in an associated sequence alignment. Different coloring schemes can be applied. Multalign Viewer reads alignments in several formats and automatically associates them with structures in Chimera, allowing for a few residue mismatches. A variety of conservation measures are available. The image includes 2D labels.