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Featured Citations

The tethered peptide activation mechanism of adhesion GPCRs. Barros-Álvarez X, Nwokonko RM et al. Nature. 2022 Apr 28;604(7907):757–762.

Structural basis for the tethered peptide activation of adhesion GPCRs. Ping YQ, Xiao P et al. Nature. 2022 Apr 28;604(7907):763–770.

Mechanism of RNA polymerase I selection by transcription factor UAF. Baudin F, Murciano B et al. Sci Adv. 2022 Apr 22;8(16):eabn5725.

Structure of active human telomerase with telomere shelterin protein TPP1. Liu B, He Y et al. Nature. 2022 Apr 21;604(7906):578–583.

Structural basis of lipopolysaccharide maturation by the O-antigen ligase. Ashraf KU, Nygaard R et al. Nature. 2022 Apr 14;604(7905):371–376.

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News

December 20, 2021

The RBVI wishes you a safe and happy holiday season! See our 2021 card and the gallery of previous cards back to 1985.

December 8, 2021

The ChimeraX 1.3 production release is available. See the change log for what's new.

October 22, 2021

The ChimeraX 1.3 release candidate is available. Please try it and report any issues. See the change log for what's new.

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UCSF ChimeraX

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 ChimeraX commercial licensing.

ChimeraX is developed with support from National Institutes of Health R01-GM129325 and the Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases.

Feature Highlight

Morphing Movie

Morphing between atomic structures can be calculated wih the morph command and played back in an animation. This movie shows morphing between two conformations of the FGFR1 kinase domain:

  • inactive structure (PDB 3c4f, chain A)
  • activated structure (PDB 3gqi, chain A) with phosphorylated tyrosines and bound ATP analog
The tyrosine side chains and ATP analog are color-coded by element: light blue carbon, red oxygen, blue nitrogen, and orange phosphorus.

Morphing and other setup was done with the command file kmorph-prep.cxc, followed by interactively positioning the structure and saving the view with the command view name p1 (generally a session would also be saved at this point), then running kmorph-play.cxc to add 2D labels and record the movie.

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Example Image

HIV-1 protease B-factor coloring

B-factor Coloring

Atomic B-factor values are read from PDB and mmCIF input files and assigned as attributes that can be shown with coloring and used in atom specification. This example shows B-factor variation within a structure of the HIV-1 protease bound to an inhibitor (PDB 4hvp). For complete image setup, including positioning, color key, and label, see the command file bfactor.cxc.

Additional color key examples can be found in tutorials: Coloring by Electrostatic Potential, Coloring by Sequence Conservation

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