Structural basis for strand transfer inhibitor binding to HIV intasomes. Passos DO, Li M et al. Science. 2020 Feb 14;367(6479):810-814.
Structure of an active human histone pre-mRNA 3'-end processing machinery. Sun Y, Zhang Y et al. Science. 2020 Feb 7;367(6478):700-703.
Volatile and thermally stable polymeric tin trifluoroacetates. Bačić G, Rankine CD et al. Inorg Chem. 2020 Jan 21;59(2):996-1005.
Direct visualization of degradation microcompartments at the ER membrane. Albert S, Wietrzynski W et al. Proc Natl Acad Sci USA. 2020 Jan 14;117(2):1069-1080.
Structural basis of substrate recognition by a polypeptide processing and secretion transporter. Kieuvongngam V, Olinares PDB et al. eLife. 2020 Jan 14;9. pii: e51492.(Previously featured citations...)
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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, nonprofit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI), supported in part by the National Institutes of Health (P41-GM103311).
UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the RBVI, following UCSF Chimera.
Axes, planes, and centroids can be calculated from sets of atoms using the Axes/Planes/Centroids tool or the command define. Axes can be shown as cylinders, planes as disks, and centroids as spheres, and any of these can be used in distance and angle measurements.
For example, the figure shows the dopamine D3 receptor and bound inhibitor (PDB entry 3pbl) as modeled into the membrane in the OPM database. The planes of the inner and outer membrane boundaries are shown as transparent blue and red disks, respectively. The protein ribbon is rainbow-colored from blue at the N-terminus to red at the C-terminus, and the axis of each helix is shown as a cylinder of matching color. The axis of the red helix forms an angle of 15.1° with the membrane and comes within 3.5 Å of the inner boundary. The yellow and orange helices are nearly antiparallel (crossing angle 5.9°). The average (minimum, maximum) distance of inhibitor atoms from the outer boundary is 7.9 (5.1, 11.7) Å.(More features...)
Potassium channel (Protein Data Bank entry 1bl8) on a dark slate blue background with potassium ions shown in firebrick. The channel is comprised of four chains. Each chain has been rainbow-colored from blue at the N-terminus to red at the C-terminus, but only the surface of the channel is shown. The surface has been sliced with a per-model clipping plane. The surface cap color is plum except with opacity set to 0.8. The shininess and brightness have been set to 128 and 8, respectively, and the lights on the scene have been moved from their default positions. The subdivision quality (related to the smoothness of the spherical ions) is 5.0, and the molecular surface was computed with probe radius and vertex density set to 1.0 and 6.0, respectively. (More samples...)
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