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See also: RCSB PDB ImagesNews
December 11, 2020
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November 4, 2020
New paper online: UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Pettersen EF, Goddard TD, et al. Protein Sci. 2020, in press.
September 23, 2020
Mac users: ChimeraX v1.1 does not work on MacOS 11.0 (Big Sur), but this problem has been fixed in v1.1.1 and the daily build.
Previous news...Upcoming Events
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
Molecular lipophilicity potential (MLP) can be calculated for a protein
and displayed with surface coloring using the command
mlp or the
Molecule Display
icon
.
The image shows the photosynthetic reaction center from a
purple sulfur bacterium, with MLP coloring on the molecular surface
and membrane boundaries from OPM (Orientations of Proteins in Membranes
entry 1eys).
Blue and red balls represent the cytoplasmic and periplasmic sides
of the bacterial inner membrane, respectively.
Parts of the L, M, and H chains span the membrane,
whereas the cytochrome subunit sits on the periplasmic side, at the top.
The surface coloring ranges from dark goldenrod for the most hydrophobic
potentials, through white, to dark cyan for the most hydrophilic.
Ligands including lipid, detergent, heme, and various other cofactors
are shown as purple surfaces.
For image setup after the structure from OPM has been opened, see the command file mlp.cxc.
More features...Example Image
The outer-membrane protein CymA admits bulky molecules into the periplasmic space of Klebsiella oxytoca. Here, CymA (PDB 4d5d chain A) is depicted in a style reminiscent of a diagnostic X-ray, with transparent molecular surface and β-strand “ribs” in white. The protein has ingested α-cyclodextrin (top) and β-cyclodextrin (bottom), bound at the entry site and near the exit, respectively. Cyclodextrin carbon atoms are shown in blue-gray and oxygen atoms in brick red. For image setup, see the command file xray.cxc.
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