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Recent Citations

Structure of the trehalose-6-phosphate phosphatase from Brugia malayi reveals key design principles for anthelmintic drugs. Farelli JD, Galvin BD et al. PLoS Pathog. 2014 Jul 3;10(7):e1004245.

Regulation of the mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement. Budkevich TV, Giesebrecht J et al. Cell. 2014 Jul 3;158(1):121-31.

Protruding knob-like proteins violate local symmetries in an icosahedral marine virus. Gipson P, Baker ML et al. Nat Commun. 2014 Jul 2;5:4278.

Enhancing UCSF Chimera through web services. Huang CC, Meng EC et al. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W478-84.

Structural rearrangements of a polyketide synthase module during its catalytic cycle. Whicher JR, Dutta S et al. Nature. 2014 Jun 26;510(7506):560-4.

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Chimera Search

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May 13, 2014

Chimera production release 1.9 is now available. See the release notes for new features since the 1.8 release series.

April 23, 2014

A production release candidate (version 1.9) is now available; please try it and report any problems. See the release notes for changes relative to the previous release.

October 31, 2013

Chimera production release 1.8.1 is now available. Changes since 1.8 are mainly to fix problems with Mac OS X 10.9 (Mavericks). See the release notes for further details and for a list of new features since the 1.7 release.

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Upcoming Events

UCSF Chimera is a highly 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 animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics, funded by the National Institutes of Health (NIGMS P41-GM103311).

Feature Highlight

Ramachandran plot 1jfuA 1jfu chain A

Ramachandran Plot

Protein backbone angles can be shown in a Ramachandran Plot along with probability contours (green lines) from a reference set of well-determined structures. Each amino acid residue is shown as a dot in a graph of φ vs. ψ, more commonly known as a Ramachandran plot or Ramachandran map. Residues are shown as blue dots, or when selected, as red dots. In the example, all helix residues have been selected. Conversely, clicking a dot in the plot will select the corresponding residue in the structure. When the plot has mouse focus, the cursor position (x = φ, y = ψ) is reported under the plot.

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Gallery Sample

Annotated Green Fluorescent Protein

BILD format was used in Chimera to annotate the barrel structure of green fluorescent protein with its centroid, major axis (red arrow), and an enclosing cylinder (shown with green hoops). The BILD file green.bild was generated with the python program green.py using the coordinates in green.pdb. Gallery entry courtesy of Mike Ess, NCRR Yeast Resource Center, University of Washington. (More samples...)