UCSF Chimera offers 3-D visualization of molecular structures and related data, including density maps, super molecular assemblies, molecular dynamics trajectories, and multiple sequence alignments. The user can also create images and animations for publication and presentation. Besides supporting core visualization, the software is specifically designed for extensibility, to allow outside developers to incorporate new desirable functions. UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments. High-quality images and animations can be generated. Chimera includes complete documentation and is free of charge for academic, government, nonprofit, and personal use. Chimera development was supported by the National Institutes of Health.
Rich set of features accessible through both commands and graphical interfaces
Visualization of molecular data on all scales, including large molecular assemblies
Integrated sequence and structure views
Production of high-quality images and movies for publication and presentation
Designed to accommodate outside development of software extensions
Broad use for academic and industry researchers, educators, and students
automatic identification of atom
hydrogen addition and partial charge assignment
high-quality hydrogen bond, contact, and clash detection
measurements include distances, angles, surface area, volume
calculation of centroids, axes, planes and associated measurements
amino acid rotamer libraries, protein Ramachandran plot, protein contact map
structure building and bond rotation
molecular dynamics trajectory playback (many formats), distance and angle plots
morphing between conformations of a protein or even different proteins
display of attributes (B-factor, hydrophobicity, etc.) with colors, radii
easy creation of custom attributes with simple text file inputs
ViewDock tool to facilitate interactive screening of docking results
rich set of commands, powerful specification syntax
many formats read, PDB and Mol2 written
Web and fetch from Protein Data Bank, CATH or SCOP (domains), EDS (density maps), EMDB (density maps), ModBase (comparative models), CASTp (protein pocket measurements), Pub3D (small molecule structures), VIPERdb (icosahedral virus capsids), UniProt (protein sequences with feature annotations)
Loading a structure into Chimera
Two methods can be used to load a structure into Chimera. 1) If the structure file is present in the user's computer, choose the menu item “File/Open”. Then select “name_of_file.pdb” and click “Open”.
The structure might also be fetched from a database, when available. Choose the menu item “File/Fetch by ID”. Choose the PDB databank and type the PDB code “name_of_file”. Then click “Fetch”.
Once the structure has been loaded, all macromolecule's bonds should appear in the “wire” representation, which is Chimera's default.
Moving / zooming
Macromolecule can be rotated by clicking the left button and dragging the cursor over Chimera's window. The translation is obtained similarly, but using the central mouse button.
Most of Chimera functionalities can be accessed by typing a given command in the “Command line”, which is situated at the bottom of the Chimera window. If the command line is not present, display it using “Favorites/Command Line”. A line precededby “Command” will appear on the lower part of the principal window.
Ribbon representation The secondary structure elements can be shown using the ribbon representation. This can be accessed through the “Actions/Ribbon” submenu.
One convenient feature of Chimera is its ability to detach
submenus so that one can use them many times without the need to go again through the different menus. For instance, choose the “Actions/Ribbon” menu item, and click on the dotted line at the top of this submenu. The submenu will be detached and freely movable.
The ribbon representation of the secondary structure elements can be switched on by choosing “show” in the “Ribbon” menu. Three variants are available: “flat”, “edged” and “rounded”.
The ribbon can be colored according to the secondary structure element, i.e. strand, helix or loop. Open the Model Panel by choosing the “Tools/Depiction/ Color Secondary Structure” menu item. This will open the “Color Secondary Structure” window.