Molecular architecture of the inner ring scaffold of the human nuclear pore complex. Kosinski J, Mosalaganti S et al. Science. 2016 Apr 15;352(6283):363-5.
Structure of promoter-bound TFIID and model of human pre-initiation complex assembly. Louder RK, He Y et al. Nature. 2016 Mar 31;531(7596):604-9.
Electronic structure of a CuII-alkoxide complex modeling intermediates in copper-catalyzed alcohol oxidations. Hayes EC, Porter TR et al. J Am Chem Soc. 2016 Mar 30;138(12):4132-45.
Force-producing ADP state of myosin bound to actin. Wulf SF, Ropars V et al. Proc Natl Acad Sci USA. 2016 Mar 29;113(13):E1844-52.
Improving functional annotation in the DRE-TIM metallolyase superfamily through identification of active site fingerprints. Kumar G, Johnson JL, Frantom PA. Biochemistry. 2016 Mar 29;55(12):1863-72.(Previously featured citations...)
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April 6, 2016
A production release candidate (v1.11) is available; please try it and report any problems. 64-bit builds are now recommended for all capable platforms, and v1.11 will be the last to support 32-bit builds. See the release notes for what's new.
July 23, 2015
Chimera production release 1.10.2 is now available. Fixes include code signing for Mac OS X installation. The 1.10 series will be the last to support OS X 10.6 and 10.7. See the release notes for details.
January 9, 2015
Chimera production release 1.10.1 is now available. 64-bit builds are recommended for all capable platforms, and the 1.10 series will be the last to support OS X 10.6 and 10.7. See the release notes for details.(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 (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. It is in early development and not yet publicly released, with release anticipated sometime in 2016.
There are several ways to superimpose structures in Chimera:
• MatchMaker performs a fit after automatically identifying which residues should be paired. Pairing uses both sequence and secondary structure, allowing similar structures to be superimposed even when their sequence similarity is low to undetectable.
The figure shows five distantly related proteins (pairwise sequence identities <25%) from the SCOP WD40 superfamily before and after MatchMaker superposition with default parameters.
• Structures can be matched using a pre-existing sequence alignment.
• The exact atoms to pair can be specified with the match command. This works on any type of structure, while the preceding methods apply only to peptide and nucleotide chains.
• Structures can be superimposed manually by activating/deactivating them for motion and using the mouse.
Side-by-side views of a potassium channel structure (Protein Data Bank entry 1bl8) showing different approaches to cavity detection. On the left are molecular surface patches corresponding to the structure's two largest pockets by MS volume in the Computed Atlas of Surface Topography of proteins (CASTp) database. On the right is a tunnel in blue identified by the MolAxis server. Simple editing converted MolAxis output into a BILD file for display in Chimera. (More samples...)