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Structure of the SecY channel during initiation of protein translocation. Park E, Ménétret JF et al. Nature. 2014 Feb 6;506(7486):102-6.
Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion. Gogala M, Becker T et al. Nature. 2014 Feb 6;506(7486):107-10.
Assessment of template-free modeling in CASP10 and ROLL. Tai CH, Bai H et al. Proteins. 2014 Feb;82 Suppl 2:57-83.
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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.
June 7, 2013
April 18, 2013(Previous news...)
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).
Given two or more superimposed structures,
Match→Align creates a corresponding sequence alignment.
The user specifies a distance cutoff for residues allowed to be
in the same column of the output alignment.
In proteins, the distances are measured between α-carbons.
The method is independent of residue types and how the
structures were superimposed.
The figure shows a superposition from MatchMaker of five proteins from the SCOP WD40 superfamily and a corresponding sequence alignment from Match→Align, automatically shown in Multalign Viewer. In the sequence alignment, light green and yellow boxes indicate strands and helices, while the headers RMSD and Conservation show spatial and sequence conservation, respectively.
Potassium channel (Protein Data Bank entry 1bl8) on a dark slate blue background with potassium ions shown in firebrick. The channel is comprised of four chains. Each chain has been rainbow-colored from blue at the N-terminus to red at the C-terminus, but only the surface of the channel is shown. The surface has been sliced with a per-model clipping plane. The surface cap color is plum except with opacity set to 0.8. The shininess and brightness have been set to 128 and 8, respectively, and the lights on the scene have been moved from their default positions. The subdivision quality (related to the smoothness of the spherical ions) is 5.0, and the molecular surface was computed with probe radius and vertex density set to 1.0 and 6.0, respectively. (More samples...)