UCSF Chimera
5269034
224849016
2008-07-10T18:13:19Z
ElaineMeng
6444453
new release version number/date, listed additional web fetch types
{{Infobox Software |
name = UCSF Chimera |
screenshot = [[Image:Chimera1.png|275px]] |
caption = Chimera main window (FSH and receptor, 1xwd) and sequence window (alignment of FSH receptors from different species). |
developer = Resource for Biocomputing, Visualization, and Informatics (RBVI), UCSF |
latest_release_version = 1.2540 |
latest_release_date = [[July 9]], [[2008]] |
operating_system = [[Microsoft Windows|Windows]], [[Mac OS X]], [[Linux]], others |
genre = [[Molecular modelling]] |
license = free for noncommercial use |
website = [http://www.cgl.ucsf.edu/chimera/index.html 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 [http://www.cgl.ucsf.edu/chimera/ImageGallery/index.html images] and [http://www.cgl.ucsf.edu/chimera/animations/animations.html movies] can be created. Chimera includes complete [http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/index.html documentation] and can be [http://www.cgl.ucsf.edu/chimera/download.html 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).
== 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), CASTp (protein pocket measurements), EDS (density maps), ModBase (comparative models), Pub3D (small molecule structures), others
== 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
== 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
== 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
== See also ==
* [[Molecular modelling]]
* [[Molecular graphics]]
* [[Molecular dynamics]]
== External links ==
* [http://www.cgl.ucsf.edu/chimera/index.html UCSF Chimera home page]
* Chimera [http://www.cgl.ucsf.edu/chimera/ImageGallery/index.html Image Gallery] and [http://www.cgl.ucsf.edu/chimera/animations/animations.html Animation Gallery]
* [http://www.cgl.ucsf.edu/chimera/docs/morerefs.html papers about Chimera ]
* [http://www.rbvi.ucsf.edu/ Resource for Biocomputing, Visualization, and Informatics]
* [http://www.ucsf.edu University of California, San Francisco]
[[Category:Molecular modelling software]]
[[Category:Bioinformatics software]]
[[Category:Free science software]]