UCSF Chimera
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| UCSF Chimera | |
|---|---|
 Chimera main window (FSH and receptor, 1xwd) and sequence window (alignment of FSH receptors from different species). |
|
| Developed by | Resource for Biocomputing, Visualization, and Informatics (RBVI), UCSF |
| Latest release | 1.2470 / November 15, 2007 |
| OS | Windows, Mac OS X, Linux, others |
| Genre | Molecular modelling |
| License | free for noncommercial use |
| Website | www.cgl.ucsf.edu/chimera |
UCSF Chimera (or simply Chimera) is an extensible program 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 movies can be created. Chimera includes complete documentation and can be downloaded free of charge for noncommercial use.
Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI) at the University of California, San Francisco. Development is funded by the NIH National Center for Research Resources (grant P41-RR01081).
Contents |
[edit] General Structure Analysis
- automatic atom type identification
- hydrogen addition and partial charge assignment
- high-quality hydrogen bond, contact, and clash detection
- distance and angle measurements, rotatable bonds
- amino acid rotamer libraries (backbone-dependent and -independent)
- molecular dynamics trajectory playback (many formats)
- clustering of conformational ensembles
- morphing between conformations of a protein or even different proteins
- display of attributes (B-factor, hydrophobicity, etc.) with colors, radii, "worms"
- easy creation of new attributes with simple text file inputs
- rich set of commands, powerful specification syntax
- many formats read, PDB and Mol2 written
- web fetch from Protein Data Bank, PQS (predicted quaternary structure), EDS (density maps), ModBase (comparative models), others
[edit] Presentation Images and Movies
- images can be saved at arbitrarily high resolution
- adjustable background color, lighting, depth-cueing, silhouette edges
- stick, ball-and-stick, sphere, ribbon, and surface displays
- nonmolecular geometric objects
- isosurfaces and transparent renderings of volume data (see below)
- arbitrary text labeling in the plane of the screen
- different structures can be clipped differently and at any angle
- optional raytracing with embedded POV-Ray
- simple graphical interface for creating movies interactively
- alternatively, movie content and recording can be scripted
- movie recording is integrated with morph and MD trajectory playback
[edit] Volume Data Tools
- many formats of volume data maps (electron density, electrostatic potential, others) read, several written
- interactive threshold adjustment, multiple isosurfaces (mesh or solid), transparent renderings
- fitting of atomic coordinates to maps and maps to maps
- density maps can be created from atomic coordinates
- markers can be placed in maps and connected with smooth paths
- display of single data planes, optionally as topographic maps
- volume data time series playback and morphing
- many tools for segmenting and editing maps
- Gaussian smoothing, Fourier transform
- surface area and surface-enclosed volume measurements
[edit] Sequence and Structure Tools
- many sequence alignment formats read, edited, written
- Newick tree format read
- automatic, mismatch-tolerant association of structures with alignment sequences
- sequence-structure crosstalk: highlighting in one highlights the other
- multiple methods for calculating conservation and displaying values on associated structures
- structure superposition using the associated sequence alignment
- in the absence of a pre-existing alignment, structure superposition using both residue type and secondary structure information
- generation of structure-based sequence alignments from superpositions of two or more proteins
