UCSF Chimera

Category Proteomics>Protein Structure/Modeling Systems/Tools

Abstract UCSF Chimera is an molecular modeling system. It can be used for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.

High-quality images and animations can be generated.

UCSF Chimera Feature/capabilities are:

Sequence Viewer -- The “Multalign Viewer” tool displays individual sequences and multiple sequence alignments. Sequence alignments can be read from external files or created by other tools in Chimera. Structures opened in Chimera are automatically associated with sufficiently similar sequences in the alignment.

After association, mousing over a residue in the sequence shows its structure residue number, selecting in the sequence selects residues in the structure(s) and vice versa, structures can be superimposed using sequence alignment.

Various measures of sequence conservation and structural variation (RMSD) can be computed and shown above the sequences as histograms, and on the structures with color or worm radius. Secondary structure elements can be depicted as colored boxes or regions on the alignment. Regions can also be created by hand.

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 (MD Movie - is a tool for viewing and analysis of trajectories and other ensembles). The morph can then be saved in coordinate form or recorded as an animation.

Molecular Graphics --

• a) Stick, ball-and-stick, CPK, ribbon, pipe-and-plank, and nucleotide display styles;
• b) Molecular surfaces;
• c) Highly intuitive rotation, translation, and scaling with the mouse;
• d) Side View for adjusting clipping planes and scaling;
• e) Interactive color editing in various color spaces (RGB, CMYK, etc.) with transparency; and
• f) ability to save high-resolution images for presentation and publication; and stereo (side-by-side and time-sequential).

Chemical Knowledge --

• a) Determination of atom types in arbitrary molecules, including non-standard residues;
• b) Ability to add hydrogen atoms;
• c) High-quality hydrogen bond identification;
• d) Selection of atoms/bonds by element, atom type, functional group, amino acid category; and interactive bond rotation, distance and angle measurements.

Showing ConSurf Results -- The ConSurf Server provides results as Chimera Web data; after browser configuration, a single click displays the color-coded query structure and multiple sequence alignment with phylogenetic tree and custom headers in a locally installed copy of Chimera.

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.

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 Protein Data Bank (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 (DOCK - addresses the problem of “docking” molecules to each other), 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 to the receptor. The Chimera extension ViewDock (software) 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 (software) 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 (software) 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.

Chimera 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 side-chains 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 (software).

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 can include 2D labels.

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 the Volume Viewer (see above...).

Volume Plane Display -- Volume data can be shown as a single plane (or slab) at a time, with the Planes feature in the 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 the 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 to show values of an attribute such as residue conservation. Opening a sequence alignment in Chimera automatically displays it in the Multalign Viewer (see above...) and associates it with any similar structures (a few residue mismatches are allowed). A variety of conservation measures can be computed.

CASTp Pocket Data -- Structures and their pocket measurements can be fetched directly from the Computed Atlas of Surface Topography of proteins (CASTp) database or read from local files previously returned by the (CASTp) server.

In Chimera, the pockets and their measurements are shown in a pocket list. Choosing one or more pockets from the list performs actions on the structure, such as zooming in on a pocket, showing its surface, and/or selecting the atoms around it.

Density Display -- Electron density maps can be displayed as mesh or solid isosurfaces with the Volume Viewer (see above...). Contour levels can be adjusted interactively, multiple levels can be shown for a given map, and the display can be restricted to a zone around specified atoms.

B-Factor Coloring -- A structure can be colored to show values of an attribute such as atomic B-factor. The image can include a molecular surface that has been clipped and capped, 2D labels, and a color key.

Structure-Based Sequence Alignment -- Given two or more superimposed structures, Match -> Align (Match -> Align - creates a sequence alignment from a structural superposition of proteins or nucleic acids in Chimera) creates a corresponding sequence alignment.

The user specifies a distance cutoff for residues allowed to be in the same column of the output alignment. In proteins, the distances are measured between a-carbons. The method is independent of residue types and how the structures were superimposed.

Superimposing Structures -- There are several ways to superimpose structures in Chimera - MatchMaker (software) performs a fit after automatically identifying which residues should be paired. Pairing uses both sequence and secondary structure, allowing similar structures to be superimposed even when their sequence similarity is low to undetectable.

Nucleotides -- Special representations of DNA and RNA can be displayed with the Nucleotides tool or the command ‘nucleotides’. Different levels of abstraction are available.

Thermal Ellipsoids -- Anisotropic B-factors can be shown as ellipsoids, with ellipsoid axes and radii representing the eigenvectors and eigenvalues of the atomic mean-square displacement matrix.

Anisotropic B-factors can be read from the input coordinate file (for example, from ANISOU records in a PDB file) and can be displayed with the tool Thermal Ellipsoids or the command ‘aniso’.

Blast Protein -- The Blast Protein tool performs a Basic Local Alignment Search Tool (BLAST) or Position Specific Iterative BLAST (PSI-BLAST) search of the PDB or NR protein database for sequences similar to a query, using a Web service hosted by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI).

The query can be:

• a) A chain from a structure open in Chimera;
• b) A sequence pasted as plain text; or
• c) A sequence from an alignment in the Multalign Viewer (see above...).

The output is a list of hits, from which all or a user-chosen subset can be retrieved:

• a) As a pseudo-multiple sequence alignment (a consolidation of the pairwise alignments of individual hits to the query), automatically shown in the Multalign Viewer; and
• b) As structures (for hits from the PDB), automatically superimposed according to the pseudo-multiple alignment.

System Requirements

Contact manufacturer.

Manufacturer

• Resource for Biocomputing, Visualization, and Informatics (RBVI)
• Computer Graphics Laboratory
• University of California San Francisco (UCSF)
• 185 Berry Street, Suite 4603
• San Francisco, California 94107 USA

Manufacturer Web Site UCSF Chimera

Price Contact manufacturer.

G6G Abstract Number 20708

G6G Manufacturer Number 104280