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Balanced plant helper NLR activation by a modified host protein complex. Huang S, Wang J et al. Nature. 2025 Mar 13;639(8054):447–455.
Activation and inhibition mechanisms of a plant helper NLR. Xiao Y, Wu X et al. Nature. 2025 Mar 13;639(8054):438–446.
A widespread plant defense compound disarms bacterial type III injectisome assembly. Miao P, Wang H et al. Science. 2025 Feb 28;387(6737):eads0377.
RNA control of reverse transcription in a diversity-generating retroelement. Handa S, Biswas T et al. Nature. 2025 Feb 27;638(8052):1122–1129.
Hierarchical design of pseudosymmetric protein nanocages. Dowling QM, Park YJ et al. Nature. 2025 Feb 13;637(8050):553–561.
Previously featured citations...Chimera Search
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March 6, 2025
Chimera production release 1.19 is now available, fixing the ability to fetch structures from the PDB (details...).
December 25, 2024
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October 14, 2024
Planned downtime: The Chimera and ChimeraX websites, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable starting Monday, Oct 14 10 AM PDT, continuing throughout the week and potentially the weekend (Oct 14-20).
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UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments. It is available free of charge for noncommercial use. Commercial users, please see Chimera commercial licensing.
We encourage Chimera users to try ChimeraX for much better performance with large structures, as well as other major advantages and completely new features in addition to nearly all the capabilities of Chimera (details...).
Chimera is no longer under active development. Chimera development was supported by a grant from the National Institutes of Health (P41-GM103311) that ended in 2018.
Feature Highlight
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.
(More features...)Gallery Sample
BILD format was used in Chimera to annotate the barrel structure of green fluorescent protein with its centroid, major axis (red arrow), and an enclosing cylinder (shown with green hoops). The BILD file green.bild was generated with the python program green.py using the coordinates in green.pdb. Gallery entry courtesy of Mike Ess, Yeast Resource Center, University of Washington. (More samples...)
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