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Recent Citations
Sellers BD, Zhu K et.al. Toward better refinement of comparative models: predicting loops in inexact environments. Proteins. 2008 Aug 15;72(3):959-71.
Lawson CL, Dutta S et.al. Representation of viruses in the remediated PDB archive. Acta Crystallogr D Biol Crystallogr. 2008 Aug;64(Pt 8):874-82.
Fromer M, Yanover C A computational framework to empower probabilistic protein design. Bioinformatics. 2008 Jul 1;24(13):i214-22.
(Previously featured citations...)Chimera Search
Google™ SearchNews
August 5, 2008
The ConSurf Server now provides results as Chimera Web data: a single click displays the color-coded query structure and multiple sequence alignment in a locally installed copy of Chimera (screen shot).
July 9, 2008
Chimera production release v1.2540 is now available. Changes since the previous production release (v1.2470, Nov 2007) are detailed in the release notes.
July 1, 2008
Current daily builds are candidates for the upcoming production release. Exceptions are the Mac Aqua and Linux OSMESA (off-screen rendering) versions, which will remain "development" for now. Please try the release candidates and report any problems.
(Previous news...)Upcoming Events
August 21, 2008
UCSF Library Course: Exploring Protein Similarity Networks with Cytoscape, UCSF Chimera, and SFLD will be offered on Tuesday, August 21 from 9am-11am at the UCSF Mission Bay Campus. This session will cover the tools and methods that have been developed at UCSF to explore protein similarity networks. Topics include:
Experience with Cytoscape required. [sign up]
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 and funded by the NIH National Center for Research Resources (grant P41-RR01081). (More about Chimera...)
Feature Highlight
The Sequence tool
shows the sequence of each chain in a structure
– the example contains both protein and DNA.
In the sequence, protein helix and strand segments are colored gold and green,
respectively, and specific patterns can be identified.
Sequence and structure are linked:
•
mousing over a residue in the sequence shows its structure residue number
•
selecting in the sequence selects residues in the structure and vice versa
See also the
sequence alignment viewer.
Gallery Sample
The image shows interactions of the delta-1 loop with the rest of hepatitis C virus RNA-dependent RNA polymerase (Protein Data Bank entry 1quv). Loop residues in contact with the rest of the structure (van der Waals overlap ≥ 0.01 Å) are displayed as sticks; interacting surface atoms are shown as red patches. (More samples...)