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Recent Citations
Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex. Guo TW, Bartesaghi A et al. Cell. 2017 Oct 5;171(2):414-426.e12.
The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus. Matzov D, Aibara S et al. Nat Commun. 2017 Sep 28;8(1):723.
Actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes. Fritz-Laylin LK, Riel-Mehan M et al. eLife. 2017 Sep 26;6. pii: e26990.
GaudiMM: A modular multi-objective platform for molecular modeling. RodrÃguez-Guerra Pedregal J, Sciortino G et al. J Comput Chem. 2017 Sep 15;38(24):2118-2126.
Structural basis of MsbA-mediated lipopolysaccharide transport. Mi W, Li Y et al. Nature. 2017 Sep 14;549(7671):233-237.
(Previously featured citations...)Chimera Search
Google™ SearchNews
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!
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).
(Previous news...)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
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.
Gallery Sample
Large ribosomal RNA is shown with individual bases depicted using solvent excluded molecular surfaces. Bases A, C, G, U are colored red, yellow, green, and blue. The surfaces were made with the Chimera multiscale tool in combination with the nucleic acid blobs plug-in. The image was raytraced using POVray.
Protein Data Bank model 1s72.
(More samples...)