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UCSF ChimeraX

UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.

ChimeraX development is funded by the National Institutes of Health (NIGMS P41-GM103311).

See also: ChimeraX Advantages

Feature Highlights

5v8m chain network screenshot

Interactive Chain Network

Chain-chain interfaces can be identified by buried surface areas and displayed as a network diagram with the interfaces command. In the diagram, nodes (circles) represent chains, larger for greater surface areas, and edges (lines) between nodes represent chain-chain interfaces (default ≥ 300 Å2 buried area). Dotted lines represent interfaces smaller than half the size of the largest in the structure. Diagram context menus enable a variety of actions, such as “exploding” the structure by moving chains apart, hiding all but the chains in contact with a given chain, and showing a more detailed plot of the residues forming a given interface.

The structure is an HIV envelope glycoprotein trimer bound by three copies of a broadly neutralizing antibody (PDB 5v8m), with chain information shown in the Log. Glycosylations (not displayed) were included in the surface area calculations. For setup, see the command file trimer-network.cxc.

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3w1k assembly 1

Assemblies from mmCIF Symmetry Information

Multimeric assemblies defined in a structure's mmCIF file are automatically listed when the file is opened and can be reconstituted with the sym command. The complex of selenocysteine synthase and tRNASec (PDB 3w1k) is shown as molecular surfaces of different colors for different chains. The asymmetric unit is on the left and the assembly specified in the mmCIF file is on the right, with arrow and text annotations from 2dlabels. See the command file sym.cxc.

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2ptt interchain H-bonds screenshot

Interactive H-Bond Histogram

Hydrogen bonds (H-bonds) can be identified with the command hbonds and plotted as an interactive histogram with the command crosslinks histogram.

The ChimeraX graphics window shows the complex between a natural killer cell receptor 2B4 and its ligand CD48 (PDB 2ptt). The receptor protein is blue, the ligand protein pink, and H-bonds between them dashed yellow, with H-bonding residues labeled. Although not done here, the H-bonds could also be labeled by distance.

The histogram of H-bond distances on the top right is interactive: when the cursor is placed over a bar in the histogram, the corresponding H-bonds are temporarily enlarged in the 3D view and the others hidden. For image setup other than orientation, see the command file hb3.cxc.

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Paired-10 palette
PuOr-5 palette

Color Palettes

A “palette” or ordered series of colors is used to color items sequentially (rainbow) or by values such as density. The ten chains in PDB 5o3l (paired tau filament) have been colored with the commands shown as 2D labels in the images. The first two examples at left use predefined palettes (credit to www.ColorBrewer.org, color specifications and designs by Cynthia A. Brewer, Pennsylvania State University), whereas the third shows specifying colors individually.

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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, then running kmorph-play.cxc to add 2D labels and record the movie.

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DNA/protein complex with struts

Struts for 3D Printing

Structures can be reinforced for 3D printing with pseudobonds. In this DNA-transcription factor complex (PDB 5ego), proteins are shown as ribbons and the DNA as a molecular surface. The pseudobonds in blue were read in from a manually created file, 5ego.pb, and further reinforcements in light gray were added automatically with the struts command. For image setup other than orientation, see the command file struts.cxc.

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membrane protein with lipophilicity coloring

Coloring by Molecular Lipophilicity Potential

Molecular lipophilicity potential (MLP) can be calculated for a protein and shown with surface coloring using the command mlp. The outer-membrane protein CymA allows the diffusion of bulky molecules into the periplasmic space of Klebsiella oxytoca. The image shows CymA (PDB 4d5d chain A) with an α-cyclodextrin molecule (purple) bound at the entry site; a β-cyclodextrin molecule (not visible) is bound inside, near the other end of the pore. The surface coloring ranges from dark goldenrod for the most hydrophobic potentials, through white, to dark cyan for the most hydrophilic. This coloring and the binding of detergent molecules (pink) together help to identify the membrane-embedded portion of the protein. For image setup other than orientation, see the command file mlp.cxc.

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AMPA receptor with tube helices

Curved Helix Cylinders

Protein α-helices can be shown as curved-cylinder “tubes“ with the cartoon style command. Helix tube mode is an alternative to the standard spiraling ribbons, and both modes are fully integrated with coil and β-strand cartoons. The structure at left is an AMPA-subtype glutamate receptor bound to the antiepileptic drug perampanel (PDB 5l1f). The receptor is tetrameric, and each chain is rainbow color-coded from blue at the N-terminus to red at the C-terminus. Four molecules of perampanel (pink) are bound near the bottom, between the transmembrane domain and the rest of the receptor. For image setup other than orientation, see the command file ampar.cxc.

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4hhb ambient lighting

Ambient Occlusion Lighting

Several lighting modes are available, including ambient occlusion. The image shows hemoglobin (PDB 4hhb) with the four chains shown as surfaces of different colors and heme residues as spheres. The command lighting soft or the Graphics “sugar cube” icon can be used to turn on ambient shadowing from 64 directions. The command lighting gentle gives a similar result, except tuned to emphasize larger indentations.

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