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Recent Citations

Structural basis of the day-night transition in a bacterial circadian clock. Tseng R, Goularte NF et al. Science. 2017 Mar 17;355(6330):1174-1180.

Structures of the cyanobacterial circadian oscillator frozen in a fully assembled state. Snijder J, Schuller JM et al. Science. 2017 Mar 17;355(6330):1181-1184.

Double-stranded RNA virus outer shell assembly by bona fide domain-swapping. Sun Z, El Omari K et al. Nat Commun. 2017 Mar 13;8:14814.

Molecular architecture of the major membrane ring component of the nuclear pore complex. Upla P, Kim SJ et al. Structure. 2017 Mar 7;25(3):434-445.

Self-assembly of nanoparticles into biomimetic capsid-like nanoshells. Yang M, Chan H et al. Nat Chem. 2017 Mar;9(3):287-294.

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Chimera Search

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December 2, 2016

Chimera production release 1.11.2 is now available. This version has been updated to work with changes in NCBI Blast and to avoid crashes on Mac Sierra (see the release notes for details).

September 24, 2016

Production release candidate (version 1.11.2) is available, superseding 1.11.1. The new version has been updated to work with changes in NCBI Blast (see release notes). Please try it and report any problems.

August 27, 2016

A production release candidate (version 1.11.1) is now available. Please try it and report any problems. See the release notes for what's been fixed since 1.11. The 1.11 release series will be the last to support 32-bit builds.

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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, 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

G Protein Interface Surface

Heterotrimeric G protein (Protein Data Bank entry 1gg2) with the alpha subunit shown in green, the beta subunit in light blue, and the gamma subunit in brown. The Intersurf tool was used to show the interface between the alpha and beta subunits. The interface surface is colored to show the distance between atoms across the interface (red for closer together, blue for farther apart). (More samples...)