about
projects
people
publications
resources
resources
visit us
visit us
search
search
Quick Links
Featured Citations
Complex water networks visualized by cryogenic electron microscopy of RNA. Kretsch RC, Li S et al. Nature. 2025 Jun 5;642(8066):250–259.
BRAF oncogenic mutants evade autoinhibition through a common mechanism. Lavoie H, Jin T et al. Science. 2025 May 29;388(6750):eadp2742.
MFSD6 is an entry receptor for enterovirus D68. Varanese L, Xu L et al. Nature. 2025 May 29;641(8065):1268–1275.
BMAL1-HIF2A heterodimer modulates circadian variations of myocardial injury. Ruan W, Li T et al. Nature. 2025 May 22;641(8064):1017-1028.
Glutamate gating of AMPA-subtype iGluRs at physiological temperatures. Kumar Mondal A, Carrillo E et al. Nature. 2025 May 15;641(8063):788–796.
More citations...News
May 7, 2025
The ChimeraX 1.10 release candidate is available – please try it and report any issues. See the change log for what's new.
March 19, 2025
|
March 1, 2025
Upcoming Events
June 24, 2025
PDB101 1-hr online tutorial: Introduction to molecular animation at 1pm Eastern, 10am Pacific: (requires registration)
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.
Feature Highlight
Axes, planes, and centroids can be defined from sets of atoms using the
Axes/Planes/Centroids tool
or the command
define.
The image shows the β2-adrenergic receptor
in inactive (gray) and activated (pink) conformations,
PDB 2rh1
and 4lde
respectively. Hydrophobic membrane boundaries (light tan) are from the
Orientations of Proteins in Membranes (OPM) database.
Plane objects were calculated from the membrane-boundary pseudoatoms in
4lde-OPM.pdb.
Axes were calculated for the α-helices in both structures
and rainbow-color-coded from blue at the N-terminus to red at the
C-terminus. Centroids (magenta) were calculated from the two ring systems
of the agonist in the activated structure.
For image setup other than position, see the command file
axes-gpcrs.cxc.
Distances and angles between the defined objects can be measured using the
Axes/Planes/Centroids tool
or commands, for example, to reveal that the ring systems of the agonist
are about 9 Å apart and 3.3 and 8.7 Å from the outer membrane
boundary; that upon activation, TM6 (gold axes) tilts by about 15°
away from the helix bundle; and that TM4 (green axes, left side of image) makes
an angle of about 80-85° with the membrane (see
axes-measurements.cxc).
Example Image
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
Axes, Planes, and Centroids
B-factor Coloring
About RBVI | Projects | People | Publications | Resources | Visit Us
Copyright 2018 Regents of the University of California. All rights reserved.