UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.
cryoEM Ambient Occlusion
A cryoelectron microscopy map of the 26S proteasome (EMD-4321) is shown at the author-recommended contour level in two different lighting modes: “simple” on the left and “soft” on the right. Soft lighting includes ambient lighting and shadowing (occlusion) and can be turned on with the command lighting soft or by clicking the Graphics sugar-cube icon.
For setup of the righthand image, see the command file ambient.cxc.More features...
ChimeraX virtual reality works with HTC Vive, Oculus Rift, and Samsung Odyssey systems (those supported by SteamVR). Any structures, maps, etc. that can be displayed in ChimeraX can be viewed in the headset and manipulated with the hand controllers. Icon toolbars visible in the headset allow changing the scene display or hand-controller button assignments with a single click. Besides rotation, translation, and zooming, useful functions include labeling, distance measurement, bond rotation, placing markers into a map, and changing map contour levels. Virtual-reality (VR) mode can be turned on and off with the vr command, and the meeting command allows multiple users to share a single session in VR.More features...
Cartoon dimensions and shape can be controlled with the command cartoon style. A few possibilities are shown here; alias is convenient for reusing settings, but the cartoon style commands could also be used directly:
alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6
alias cylinders cartoon style protein modeh tube rad 2 sides 24
alias licorice car style protein modeh default arrows f xsect oval width 1 thick 1
|initial cartoon style
+ nuc stubs
|nucrib + cylinders
(protein α-helix tubes)
|nucrib + licorice
(no 2°-structure representations)
Interactive H-Bond 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.More features...
Coloring by Molecular Lipophilicity Potential
Molecular lipophilicity potential (MLP) can be calculated for a protein and displayed with surface coloring using the command mlp. 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...
Special representations of nucleotide sidechains can be shown with the nucleotides command. Options include slabs for bases (box, muffler, or ellipsoid shape), bumps on slabs to show base orientation, simple tubes instead of ribose atoms, and continuous or broken ladder rungs. Several possibilities are shown for a base pair in PDB 1bna (from left to right, DG 22 and DC 3). Nucleotide representations can be the same color as the ribbon or a different color; slabs and ladder half-rungs are colored to match the C2 atom of the corresponding base, and ribose tubes are colored to match the C1' atom. Multiple nucleotide styles can be used within a single structure.More features...
Multichannel Light Microscopy
3D images and time series from multichannel optical microscopy are shown in the Volume Viewer tool, with easy access to hiding/showing individual channels, changing their colors, and adjusting threshold levels with the mouse. The menu of style options includes “volume” (translucent blobs, as in the image), surface, mesh, maximum intensity projection, single plane, and orthoplanes. For convenience, the step size, region bounds, and display style of different channels of the same dataset are coupled, in that changing the setting of one channel automatically changes it for the others.
The image shows human induced pluripotent stem cells, with plasma membrane in violet red, EGFP-tagged fibrillarin (as a marker for nucleolus) in yellow, and DNA (nucleus) in turquoise. The data are publicly available from the Allen Cell Explorer website, dataset: AICS-14_0.More features...
Fitting to Density Maps
Atomic structures and/or maps can be fit rigidly into other maps with the fitmap command. A common use is to locally optimize the fit after initial placement by hand. Options include symmetrical and sequential fitting, as well as global search to generate multiple starting points for local optimization.
Elongator is a highly conserved complex that associates with RNA polymerase II during transcriptional elongation. In the image, one of its six subunits, Elp2 (PDB 5m2n), has been fit into a map of the Elp123 subcomplex (EMDB 4151).More features...
The matchmaker command is convenient for superimposing related structures without having to worry about numbering or missing residues. It superimposes proteins (and nucleic acids) by creating a pairwise sequence alignment, then matching the sequence-aligned residues in 3D. Secondary structure helps guide the sequence alignment for better performance on more distantly related proteins with harder-to-align sequences. By default, the fit is iterated to exclude structurally dissimilar regions and superimpose the most similar parts more closely.
The resulting sequence alignments can be displayed, as in this example of three pectate lyases: PDB 1jta, 1bn8, and 2pec. In the sequence alignments, residues used in the final fit iteration are enclosed in light orange boxes. RMSD values and other fit statistics are reported in the Log. For setup other than structure orientation, see the command file peclyases.cxc.More features...
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.More features...
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.More features...
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.More features...
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
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.More features...
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.More features...
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.More features...
Ambient Occlusion Molecular Surfaces
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.More features...