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Recent Citations

Structure of the yeast spliceosomal postcatalytic P complex. Liu S, Li X et al. Science. 2017 Dec 8;358(6368):1278-1283.

Structural insight into the rearrangement of the switch I region in GTP-bound G12A K-Ras. Xu S, Long BN et al. Acta Crystallogr D Struct Biol. 2017 Dec 1;73(Pt 12):970-984.

3.9 Å structure of the yeast Mec1-Ddc2 complex, a homolog of human ATR-ATRIP. Wang X, Ran T et al. Science. 2017 Dec 1;358(6367):1206-1209.

Structural basis for the initiation of eukaryotic transcription-coupled DNA repair. Xu J, Lahiri I et al. Nature. 2017 Nov 30;551(7682):653-657.

Primer synthesis by a eukaryotic-like archaeal primase is independent of its Fe-S cluster. Holzer S, Yan J et al. Nat Commun. 2017 Nov 23;8(1):1718.

(Previously featured citations...)

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News

October 24, 2017

Chimera production release 1.12 is now available (64-bit builds for Windows, Mac, and Linux). See the release notes for details.

September 12, 2017

A production release candidate (version 1.12) is available; please try it and report any problems. See the release notes for what's new.

March 13, 2017

For a nice 3D-printing protocol that uses Chimera, see 3D Printing of Biomolecular Models for Research and Pedagogy by Da Veiga Beltrame, Tyrwhitt-Drake, et al. today in JoVE!

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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, nonprofit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI), funded by the National Institutes of Health (NIGMS P41-GM103311).

UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the RBVI, following UCSF Chimera.

Feature Highlight

mda p08648 limit 4 percent 50

Find and Summarize Structures for a Sequence

One use of Multidomain Assembler is to set up comparative modeling and concatenation of existing structures to generate a full-length model of a multidomain protein. However, even without model-building, the byproduct is also useful: a visual summary of the structures available for a query sequence, optionally filtered by criteria such as BLAST score and % identity, laid out horizontally in approximate N→C order relative to the query. Overlapping hits are stacked vertically, and segments without structural coverage are indicated with spheres. By default, the multiple sequence alignment of the hits to the query is also displayed.

The figure shows the results of command:
    mda p08648 ~/Desktop/MDA limit 4 percent 50
with sequence mismatches in red and molecules other than the hit chains in blue. Text and pointers have been added with 2D Labels.

Multidomain Assembler is described in a paper.

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Gallery Sample

Peroxiredoxin Wreath

Peroxiredoxins are enzymes that help cells cope with stressors such as high levels of reactive oxygen species. The image shows a decameric peroxiredoxin from human red blood cells (Protein Data Bank entry 1qmv), styled as a holiday wreath.

See also the RBVI holiday card gallery.

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