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]]