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Chimera 1.9

Program for interactive visualization and analysis of molecular structures.

 

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Chimera 1.9 facilities

Vendor
Vendor`s Webhttp://www.cgl.ucsf.edu
UCSF Chimera webshot
OSWindows XP, Windows Vista, Windows 7, Mac OS, Linux, Unix
Limitationsnot specified
Actualizedmore than year ago
Downloads3804
LocalizedEnglish
LicenseOpen source
SnapshotChimera snapshot
Snapshot of Chimera

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Chimera manufacturer description

Sequence Viewer

The Multalign Viewer tool displays individual sequences and multiple sequence alignments. Sequence alignments can be read from external files (several formats) or created by other tools in Chimera. Structures opened in Chimera 1.9 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 the 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. The morph can then be saved in coordinate form or recorded as an animation.

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.

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

Showing ConSurf Results

The ConSurf Server provides results as Chimera Miscellaneous 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 download (details).

Special thanks to Elana Erez and the Ben-Tal and Pupko groups at Tel Aviv University, and to Fabian Glaser at the Technion.

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
View Dock image

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.

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.
(More features...)
volume plane topography
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.
(More features...)
surface color by density
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.
(More features...)
radial surface color
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.
(More features...)
ribbon color by conservation
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 Multalign Viewer and associates it with any similar structures (a few residue mismatches are allowed). A variety of conservation measures can be computed. The image was created using the PFAM Carb_anhydrase seed alignment PF00194_seed.slx and includes a color key and 2D labels.

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.
The figure shows the four largest pockets by volume identified by CASTp for PDB entry 1ovh, a cavity mutant of T4 lysozyme. The pocket surfaces are colored yellow, orange, pink, and magenta in order of decreasing volume. The largest (yellow) is lysozyme`s active site, with two openings. The second largest (orange) is the engineered cavity, completely enclosing a bound aniline derivative. The mutated positions are shown in red. Chloride ions are displayed as green balls.

Density Display

Electron density maps can be displayed as mesh or solid isosurfaces with Volume Viewer. Contour levels can be adjusted interactively, multiple levels can be shown for a given map, and display can be restricted to a zone around specified atoms. The image (see how-to) shows PDB entry 2fma and its electron density map. Chimera can fetch the map directly from the Electron Density Server.

B-Factor Coloring

A structure can be colored to show values of an attribute such as atomic B-factor. The image includes a molecular surface that has been clipped and capped, 2D labels, and a color key. Color Zone was used to color the planar cross-section of the surface (see image how-to).

Structure-Based Sequence Alignment

Given two or more superimposed structures, Match→Align 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 α-carbons. The method is independent of residue types and how the structures were superimposed.
The figure shows a superposition from MatchMaker of five proteins from the SCOP WD40 superfamily and a corresponding sequence alignment from Match→Align, automatically shown in Multalign Viewer. In the sequence alignment, light green and yellow boxes indicate strands and helices, while the headers RMSD and Conservation show spatial and sequence conservation, respectively.

Superimposing Structures

There are several ways to superimpose structures in Chimera:
• MatchMaker 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.
The figure shows five distantly related proteins (pairwise sequence identities
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Chimera categories

visualization, density maps, supramolecular assemblies, molecular structures, docking results, trajectories, conformational ensembles, sequence alignments

What is new in 1.9 changeinfo log

General Changes:

  • optional icon to show and control menu selection mode (Append, Intersect, Replace, or Subtract)
  • some Preferences reorganization, including new categories: Labels, Selection
  • model silhouette attribute allows showing silhouettes for specific models (previously all or none)
  • Ramachandran Plot probabilities can be assigned as a residue attribute
  • new output movie format WMV2
  • new input volume format VTK structured points, ASCII
  • new export formats COLLADA, VTK
  • more efficient save/restore of coordinates in session files (for MD trajectories or very large structures, ~5% smaller session files and 3X faster save/restore)
New Tools:
  • Align Chain Sequences (Sequence) — generate a multiple sequence alignment (MSA) of structure chains using a Clustal Omega or MUSCLE web service hosted by the UCSF RBVI
Tool Changes:
  • APBS (Surface/Binding Analysis) — by default, explicit solvent is omitted from the calculation
  • Axes/Planes/Centroids (Structure Analysis) —
    • axis, plane, and centroid objects are now surface models (improved behavior with transparency and shadows; can be recolored with Actions menu, color, scolor)
    • axes can be calculated from centroids as well as atoms
  • Build Structure (Structure Editing) —
    • can build nucleic acid double helices
    • join models (peptide bond option) allows specifying new φ angle
    • button to delete selected atoms/bonds
  • Color Key (Utilities) — tick mark length and width settings added
  • Distances (Structure Analysis) — default distance monitor color, linewidth, and line style can be saved to preferences
  • Find Clashes/Contacts (Structure Analysis, Surface/Binding Analysis) — option to display contact residues if not already shown
  • Icosahedron Surface (Higher-Order Structure) — added line-width setting for mesh
  • MD Movie (MD/Ensemble Analysis) —
    • separate settings for including or omitting alkali metal ions, other metal ions, and monatomic anions from various calculations (RMSD, clustering, averaging)
    • sessions support partly loaded trajectories
  • Minimize Structure (Structure Editing) —
    • default number of conjugate gradient steps decreased from 100 to 10
    • improved logging
  • Morph Conformations (Structure Comparison) — chain pairing uses chain IDs if the sets of IDs are identical
  • Morph Map (Volume Data) — optionally interpolates colors if the maps have the same number of coloring thresholds
  • Multalign Viewer (Sequence) —
    • sequence names can be edited
    • regular expression searching
    • protein sequences with U (selenocysteine), O (pyrrolysine) can be aligned
    • Clustal Omega or MUSCLE can be used via web service to realign the sequences
    • active region contents can be opened in a new window
  • Multiscale Models (Higher-Order Structure) — surfaces of different chains with the same sequence are colored alike
  • Rotamers (Structure Editing) — added Dynameomics rotamer library
New Commands:
  • adjust — change bond angle or bond length
  • colorkey — command-line implementation of the Color Key tool, plus direct specification of color key placement
  • leap — use a Leap Motion Controller with Chimera
  • mda — BLAST-search and retrieve structures related to a query sequence, lay them out left→right in Chimera by N→C matches to the query
  • struts — add pseudobonds to a molecule to strengthen it for 3D printing
Command Changes:
  • angle — option to report angle between 1-2 and 3-4 vectors instead of 1-2-3-4 dihedral
  • apbs —
    • by default, explicit solvent is omitted from the calculation
    • added options to use a local executable or an alternative Opal web service
  • coulombic — atoms/charges to use can be specified independently of the surface to color; this allows coloring the surface of one molecule by the potential from another, for example, or coloring nonmolecular surfaces such as density isosurfaces
  • define —
    • axis, plane, and centroid objects are now surface models (improved behavior with transparency and shadows; can be recolored with Actions menu, color, scolor)
    • axes can be calculated from centroids as well as atoms
  • findclash — option to reveal (display) contact residues if not already shown
  • matrixcopy — allows many-to-many transformation copying (previously just one-to-one or one-to-many)
  • minimize — default number of conjugate gradient steps decreased from 100 to 10; improved logging
  • morph — chain pairing uses chain IDs if the sets of IDs are identical
  • pdb2pqr — added options to use a local executable or an alternative Opal web service
  • ramachandran (undocumented in earlier versions) — can assign probabilities as a residue attribute
  • reset —
    • options such as holdSteady can be used with the default position
    • moveModels can be used without holdSteady
  • set — can enable/disable transparent background for subsequently saved images
  • swapaa — added Dynameomics rotamer library
  • vina — added options to use a local executable or an alternative Opal web service
  • volume — added options to automatically set threshold (contour) level so that the surface encloses a target spatial volume
  • vop —
    • vop morph optionally interpolates colors if the maps have the same number of coloring thresholds
    • vop maximum (new) takes pointwise maximum of input maps
    • vop multiply (new) multiplies maps, for example to apply a mask
  • vseries — added options to open and close volume series, jump playback to a specific frame, perform various types of processing such as alignment, normalization, cropping, and compression, and save to file in Chimera map format
Notable Bugfixes:
  • Write Prmtop now works when using newer force fields
  • Chimera menus and dialogs use system font size settings (tested mainly on Linux)
  • Fixed bounding box calculation for transformed VRML nodes so that when exported VRML files are read back in, they rotate correctly
  • Fixed problem with “missing structure” loop modeling that allowed an extra residue at the C-terminal end of the modeled part to move
  • Fixed locking bug in suppport for "chimera --send"
Known Bugs:
  • surfaces fail for some structures
  • crash on Mac dual display systems. Details.

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End user agreement for Chimera

UCSF Chimera Non-Commercial Software License Agreement

This license agreement ("License"), effective today, is made by and between you (hereinafter referred to as the "Licensee") and The Regents of the University of California, a California corporation having its statewide administrative offices at 1111 Franklin Street, Oakland, California 94607-5200, ("Regents") acting through its Office of Technology Management, University of California San Francisco, 185 Berry Street, Suite 4603, San Francisco, California 94107, and concerns certain software known as "UCSF Chimera," a system of software programs for the visualization and interactive manipulation of molecular models, developed by the Computer Graphics Laboratory at the University of California San Francisco for research purposes and includes executable code, source code, and documentation (hereinafter referred to as the "Software").

1. General. A non-exclusive, nontransferable, perpetual license is granted to the Licensee to install and use the Software for academic, non-profit, or government-sponsored research purposes. Use of the Software under this License is restricted to non-commercial purposes. Commercial use of the Software requires a separately executed written license agreement.
2. Permitted Use and Restrictions. Licensee agrees that it will use the Software, and any modifications, improvements, or derivatives to the Software that the Licensee may create (collectively, "Improvements") solely for internal, non-commercial purposes and shall not distribute or transfer the Software or Improvements to any person or third parties without prior written permission from the Regents. The term "non-commercial," as used in this License, means academic or other scholarly research which (a) is not undertaken for profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged in the commercial use, application or exploitation of works similar to the Software.
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