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Cryo-EM structures of the pore-forming A subunit from the Yersinia entomophaga ABC toxin. Piper SJ, Brillault L et al. Nat Commun. 2019 Apr 26;10(1):1952.
Structure reveals a mechanism of CRISPR-RNA-guided nuclease recruitment and anti-CRISPR viral mimicry. Rollins MF, Chowdhury S et al. Mol Cell. 2019 Apr 4;74(1):132-142.e5.
Protein denaturation at the air-water interface and how to prevent it. D'Imprima E, Floris D et al. eLife. 2019 Apr 1;8. pii: e42747.
Structural snapshots of 26S proteasome reveal tetraubiquitin-induced conformations. Ding Z, Xu C et al. Mol Cell. 2019 Mar 21;73(6):1150-1161.e6.
Unexpected receptor functional mimicry elucidates activation of coronavirus fusion. Walls AC, Xiong X et al. Cell. 2019 Feb 21;176(5):1026-1039.e15.
See also: RCSB PDB ImagesNews
June 6, 2019
The ChimeraX 0.9 production release is available. See the change log for what's new.
May 30, 2019
From the Rochester Institute of Technology: Student develops tool to visualize molecular dynamics of proteins in virtual reality with ChimeraX.
May 23, 2019
A ChimeraX 0.9 release candidate is available – please try it and report any issues.
Previous news...Upcoming Events
July 10, 2019
Tom Goddard will lead a ChimeraX-cryoEM session at the S2C2 Modeling Workshop (Stanford-SLAC Cryo-EM Center, July 10-12, 2019). Apply to workshop...
UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX can be downloaded free of charge for academic, government, nonprofit, and personal use. Commercial users, please see licensing.
ChimeraX development is supported in part by the National Institute of General Medical Sciences (R01-GM129325; previously P41-GM103311) and the National Institute of Allergy and Infectious Diseases.
Feature Highlight
The matchmaker command is convenient for superimposing related structures without having to worry about numbering or missing residues. It superimposes proteins (and nucleic acids) by creating a pairwise sequence alignment, then matching the sequence-aligned residues in 3D. Secondary structure helps guide the sequence alignment for better performance on more distantly related proteins with harder-to-align sequences. By default, the fit is iterated to exclude structurally dissimilar regions and superimpose the most similar parts more closely.
The resulting sequence alignments can be displayed, as in this example of three pectate lyases: PDB 1jta, 1bn8, and 2pec. In the sequence alignments, residues used in the final fit iteration are enclosed in light orange boxes. RMSD values and other fit statistics are reported in the Log. For setup other than structure orientation, see the command file peclyases.cxc.
More features...Example Image
The photosynthetic reaction center from a
purple sulfur bacterium is shown as a cartoon with “tube” helices
and membrane boundaries from the OPM database (Orientations of Proteins in Membranes,
entry 1eys).
Blue and red balls represent the cytoplasmic and periplasmic sides
of the bacterial inner membrane, respectively.
The title and other text labels were added with the
2dlabels
command and repositioned interactively with the move label
mouse mode
.
ChimeraX session file: prc.cxs
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